gebhart/patrepeval huggingface dataset:
An evaluation of detection methods for large lariat RNAs (2005)

Ty1 elements are long terminal repeat (LTR) retrotransposons that reside within the genome of Saccharomyces cerevisiae. It has been known for many years that the 2'-5' phosphodiesterase Dbr1p, which debranches intron lariats, is required for efficient Ty1 transposition. A recent report suggested the intriguing possibility that Ty1 RNA forms a lariat as a transposition intermediate. We set out to further investigate the nature of the proposed Ty1 lariat branchpoint. However, using a wide range of techniques we were unable to find any evidence for the proposed lariat structure. Furthermore, we demonstrate that some of the techniques used in the initial study describing the lariat are capable of incorrectly reporting a lariat structure. Thus, the role of the Dbr1 protein in Ty1 retrotransposition remains elusive.
Performance evaluation of a transformable axial-shift type single-ring OpenPET (2013)

One of the challenging applications of PET is implementing it for in-beam PET, which is an in situ monitoring method for charged particle therapy. For this purpose, we have previously proposed two geometries for our open-type PET scanners named OpenPET. The original OpenPET had a physically opened field-of-view (FOV) between two detector rings through which irradiation beams pass. This dual-ring OpenPET (DROP) had a wide axial FOV including the gap. But, this geometry is not necessarily the most efficient for application to in-beam PET in which only a limited FOV around the irradiation field is required. Therefore, we proposed a single-ring OpenPET (SROP) geometry which can provide an accessible and observable open space with higher sensitivity and a reduced number of detectors compared to DROP. Also, we proposed two arrangement types, a slanted ellipse (SE) type where oval detector rings are slanted and stacked and an axial shift (AS) type where block detectors originally forming a conventional PET scanner are axially shifted little by little. Previously, we developed the SE-SROP prototype, and showed its good performance for in-beam PET. However, the SE-SROP decreased sensitivity slightly relative to the ring-type PET and needed a large gantry in the axial direction for conventional PET studies. On the other hand, AS-SROP can transform conventional ring-type PET scanners into stacked detectors with a gradual axial shift. In this work, we developed and evaluated a small AS-SROP prototype for proof-of-concept. The AS-SROP prototype was designed with 2 cylinder-shaped detector rings of 16 DOI detectors. The system sensitivity and spatial resolution were measured and were 5.1% and 2.6 mm, respectively, for the OpenPET mode. For the conventional PET mode, the system sensitivity and spatial resolution were 7.3% and 2.2 mm, respectively. We concluded that the AS-SROP geometry has a good potential for not only in-beam imaging but also conventional PET studies.
Central Circulation, Peripheral Circulation and Recirculation (1997)

Review Articles| October 30 2008 Central Circulation, Peripheral Circulation and Recirculation: Why and How the Artificial Kidney and the Body Interact Subject Area: Nephrology Claudio Ronco; Claudio Ronco aDepartment of Nephrology, St. Bortolo Hospital, Vicenza, Italy; Search for other works by this author on: This Site PubMed Google Scholar Rinaldo Bellomo Rinaldo Bellomo bIntensive Care Unit, Austin and Repatriation Medical Center, Heidelberg, Vic., Australia Search for other works by this author on: This Site PubMed Google Scholar Blood Purif (1997) 15 (4-6): 334–345. https://doi.org/10.1159/000170352 Article history Published Online: October 30 2008 Content Tools Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Claudio Ronco, Rinaldo Bellomo; Central Circulation, Peripheral Circulation and Recirculation: Why and How the Artificial Kidney and the Body Interact. Blood Purif 31 December 1997; 15 (4-6): 334–345. https://doi.org/10.1159/000170352 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 JournalsBlood Purification Search Advanced Search Article PDF first page preview Close Modal This content is only available via PDF. 1997Copyright / Drug Dosage / DisclaimerCopyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. You do not currently have access to this content.
Bandpass Filter With Variable Bandwidth Based on a Tapered Fiber With External Polymer Cladding (2009)

A thermo-optical bandwidth-variable fiber-based bandpass filter is experimentally and theoretically demonstrated by simply utilizing a tapered standard single-mode fiber covered with a dispersive polymer layer. The 3-dB spectral bandwidth can be tuned from 250 to 500 nm with the filter center wavelength around 1 mum.
Upper bound for the Laplacian eigenvalues of a graph (2011)

In this note we give a new upper bound for the Laplacian eigenvalues of an unweighted graph. Let $G$ be a simple graph on $n$ vertices. Let $d_{m}(G)$ and $λ_{m+1}(G)$ be the $m$-th smallest degree of $G$ and the $m+1$-th smallest Laplacian eigenvalue of $G$ respectively. Then $ λ_{m+1}(G)\leq d_{m}(G)+m-1 $ for $\bar{G} \neq K_{m}+(n-m)K_1 $. We also introduce upper and lower bound for the Laplacian eigenvalues of weighted graphs, and compare it with the special case of unweighted graphs.
Anti-Proliferative Effect of Cytohesin Inhibition in Gefitinib-Resistant Lung Cancer Cells (2012)

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI), such as gefitinib, have been proven to efficiently inhibit the proliferation of a subset of non small-cell lung cancers (NSCLC). Unfortunately, the majority of NSCLC expressing wild type EGFR is primarily resistant to EGFR-TKI treatment. Here, we show that the proliferation of the gefitinib-resistant NSCLC cell lines H460 and A549 is reduced by the small molecule SecinH3 which indirectly attenuates EGFR activation by inhibition of cytohesins, a class of recently discovered cytoplasmic EGFR activators. SecinH3 and gefitinib showed a synergistic antiproliferative effect, which correlated with a profound inhibition of Akt activation and survivin expression. Treating mice bearing H460 xenografts with SecinH3 showed the antiproliferative and pro-apoptotic effect of SecinH3 in vivo. Our data suggest that targeting the EGFR indirectly by inhibiting its cytoplasmic activators, the cytohesins, has the potential to improve the treatment of primarily EGFR-TKI resistant lung cancers.
Simultaneous Intracochlear Stimulation Based on Channel Interaction Compensation: Analysis and First Results (2008)

A simultaneous paradigm for electric stimulation of the acoustic nerve based on a monopolar electrode configuration and sign-correlated pulses is presented. Simultaneous pulse amplitudes are determined by taking into account parameters of spatial channel interaction. The computation of simultaneous amplitudes requires the solution of linear systems of equations in an iterative procedure. The computation amount can be reduced significantly, if the spatial impulse responses in individual electrodes can be approximated by two exponentially decaying branches with decay constants alpha toward apex and beta toward base. Generally, the associated inverse of the channel interaction matrix is tridiagonal. Preliminary vowel and consonant identification tests with four cochlear implant patients have been conducted for sequential and simultaneous processor settings. For equal overall pulse repetition rates, comparable speech perception scores were obtained, when the decay constants alpha and beta were set accordingly. Theoretically, the pulse rate of an N-channel system can be increased up to a factor of N as compared to the standard sequential paradigm, and pulses with technically reasonable phase durations can be utilized.
Predictors of Insulin Resistance and Liver Steatosis in the Miami Adult Studies on HIV (MASH) Cohort (2020)

Immune activation is central to developing insulin resistance and is implicated in the pathophysiology of liver steatosis. People living with HIV (PLWH) have elevated biomarkers of immune activation, which may play a role in faster development of insulin resistance and liver steatosis. The objective of this study was to examine if HIV status and immune activation are related to insulin resistance and liver steatosis. Demographic and anthropometric data on MASH cohort participants were obtained. Insulin resistance was estimated using the triglyceride-glucose (TyG) index from fasting blood. HIV status was abstracted from participants’ medical records. Immune activation biomarkers soluble CD163 (sCD163), sCD27, sCD14, and monocyte chemoattractant protein (MCP-1) measured with multiplex flow cytometry in Dr. Sherman's laboratory. High sensitivity C-Reactive Protein (hsCRP), measure of inflammation, was determined by LabCorp. Liver steatosis was defined as liver fat >3.5% obtained with magnetic resonance elastography scans. Statistics included descriptive analysis, Mann-Whitney tests, multivariate linear, and logistic regressions, controlled for age, sex, and BMI. Of the 712 participants (age 54.24 ± 7.48 years), 336 were PLWH with suppressed viral load, and 376 were uninfected healthy participants. PLWH had higher levels of sCD27 (P = 0.003) and MCP-1 (P = 0.034) than uninfected participants. Multiple linear regressions showed HIV status and sCD163 were independently associated with higher insulin resistance (HIV status b = 0.130, P = 0.014, sCD163 Multiple logistic regressions showed higher levels of sCD163 (OR = 1.097, 95% CI: 1.01–1.19, P = 0.032) and insulin resistance (OR = 7.126, 95% CI: 2.59–19.58, P < 0.001) were significant predictors of liver steatosis. HIV status, sCD14, sCD27, hsCRP, or MCP-1 were not related to liver steatosis. These results indicate that HIV infection and sCD163, a marker of immune activation, are independent predictors of insulin resistance, and sCD163 was associated with greater odds of liver steatosis. Lifestyle interventions and anti-inflammatory agents aimed at reducing insulin resistance and immune activation in PLWH may help to reduce the risk of liver steatosis and other co-morbidities. Grant Number: U01DA040381.
Analysis of radar images by means of digital terrain models (1984)

It is pointed out that the importance of digital terrain models in the processing, analysis, and interpretation of remote sensing data is increasing. In investigations related to the study of radar images, digital terrain models can have a particular significance, because radar reflection is a function of the terrain characteristics. A procedure for the analysis and interpretation of radar images is discussed. The procedure is based on a utilization of computer simulation which makes it possible to produce simulated radar images on the basis of a digital terrain model. The simulated radar images are used for the geometric and radiometric rectification of real radar images. A description of the employed procedures is provided, and the obtained results are discussed, taking into account a test area in Northern California.
Microstructuring conducting polymers and molecularly imprinted polymers by light-activated electropolymerization on micromachined silicon. Applications in electrochemical sensing (2013)

Light-activated electropolymerization on micromachined n-type silicon is here demonstrated to be a versatile route for microstructuring conducting polymers (CPs) and CP-based Molecularly Imprinted Polymers (MIPs). Several CPs - namely polypyrrole (PPy), poly(3,4-ethylendioxythiophene) (PEDOT), poly(3-methylthiophene) (P3MT), polythiophene (PT) - and a PPy-based MIP have been deposited on different microstructured n-type silicon templates featuring ordered-array of pores with variable aspect-ratio (AR) between 1 and 10. CP and MIP microtubes with size of a few micrometers, height from 5 up to 50 micrometers, and period of a few micrometers are successfully synthesized by replication of the silicon template features with submicrometer accuracy, as demonstrated by scanning electron microscopy (SEM). A significant electroactivity increase is observed for CP microtubes thanks to the augmented surface of microstructured films, as highlighted by cyclic voltammetry (CV), thus demonstrating that the entire microstructured polymer surface is effectively involved in electrochemical redox processes. PPy-based MIPs for the antibiotic sulfadimethoxine (SDM) exhibit good sensing properties in SDM electrochemical detection, with current responses notably higher than Not-Imprinted Polymers (NIPs). A significant current response increase on microstructured MIPs with respect to the flat ones is also verified.
Stable preservation of hemoglobin vesicles as a blood substitute (1999)

Long-term preservation of hemoglobin (Hb) vesicles, the so-called artificial red cell (ARC), in dry powder was studied. Carbonylhemoglobin (COHb) was encapsulated in the vesicle of 1,2-bis(2,4-octadecadienoyl)-sn-glycero-3-phosphocholine (DODPC) and the polymerizable membrane components were polymerized by γ-ray irradiation. The obtained ARC suspension was then freeze-dried in the presence of sucrose. The factors influencing the shelf-life of the freeze-dried ARC, such as sucrose concentration, moisture and storage temperature, were elucidated. After storage in the dry state for more than one year, the oxygen-carrying capacity was recovered by rehydration of the freeze-dried ARC with distilled water and substitution of the carbon monoxide ligand with oxygen. Copyright © 1999 John Wiley & Sons, Ltd.
Single or Multiple HLA-A, B, C or DRB1 Mismatches Limit Success of Unrelated Donor Bone Marrow Transplantation. (2006)

Abstract Fewer than 50% of patients (pts) are able to identify an HLA-A, B, C, DRB1-sequence matched unrelated donor (URD); the best partially matched donor must be chosen for the remainder. National Marrow Donor Program data from 3860 US transplants performed from 1988–2003 were analyzed to provide guidance in that choice. Pts had AML, ALL, CML or MDS and received myeloablative conditioning regimens. Most received calcineurin-based GVHD prophylaxis with T replete grafts (79%). Nearly all received marrow grafts (94%). Median follow-up was 6 years. Pts and donors were retrospectively typed for HLA-A, B, C, DRB1, DQB1, DQA1, DPB1, and DPA1 by DNA sequencing and other high resolution typing methods. Matching was classified as low resolution (antigen-equivalent) or high resolution (allele sequence). Because of multiple comparisons, p-values &lt;0.01 were considered significant. All analyses were adjusted for pt and transplant characteristics. RESULTS: Full matching for HLA-A, B, C, and DRB1 was associated with the best survival. A single mismatch at A, B, C or DRB1 was associated with a mortality relative risk (RR) of 1.23 (95% CI 1.11–1.36, p=0.0001) with 1-yr survival of 45% compared to 52% for fully matched pairs. Mismatches detected by low or high DNA resolution testing were associated with similar survival decrements (p=0.7). Survival differences were apparent in all disease risk categories. When mismatches at individual HLA loci were analyzed, a single mismatch at HLA-A was significantly associated with increased mortality (RR 1.35, 95% CI 1.14–1.59, p=0.0004); isolated HLA-A, B, C or DP mismatches were associated with increased risk of grades III-IV GVHD. Although the data set had few DRB1 mismatches (no antigen level and 58 allele level) limiting the power of this analysis, the RR of mortality (1.31, 95% CI 0.96–1.79, p=0.085) suggests an adverse outcome for DRB1 mismatching equivalent to A mismatching. Isolated DQ mismatching had no adverse impact. Mismatches at 2 HLA loci were associated with higher mortality risk than single mismatches (37% vs. 45% 1-yr survival), with HLA-A+C and HLA-B+C being the most frequent. CONCLUSION: High resolution DNA typing of HLA-A, B, C, and DRB1 alleles facilitates optimal URD donor selection for pts with hematological malignancies because the best survival is associated with complete matching at these loci. When selecting among donors with single mismatches, HLA-DQ or DP disparity was not associated with worse survival. Examination of risks for mortality suggests single HLA-B or C mismatches are better tolerated than HLA-A or possibly DRB1 mismatches. Disparities for 2 loci, detected by either high or low resolution testing, compound the risk of mortality.
Effects of sub-threshold transcutaneous auricular vagus nerve stimulation on cerebral blood flow (2021)

Abstract Background Transcutaneous auricular vagus nerve stimulation (taVNS) has shown promise as a non-invasive alternative to vagus nerve stimulation (VNS) with implantable devices, which has been used to treat drug-resistant epilepsy and treatment-resistant depression. Prior work has used functional MRI to investigate the brain response to taVNS, and more recent work has also demonstrated potential therapeutic effects of high-frequency sub-threshold taVNS in rheumatoid arthritis. However, no studies to date have measured the effects of high-frequency sub-threshold taVNS on cerebral blood flow (CBF). Objective/Hypothesis The objective of this study was to determine whether high-frequency (20 kHz) sub-threshold taVNS induces significant changes in CBF. Methods Arterial spin labeling (ASL) MRI scans were performed on 20 healthy subjects in a single-blind placebo-controlled repeated measures experimental design. The ASL scans were performed before and after 15 minutes of either sub-threshold taVNS treatment or a sham control. Results taVNS induced significant changes in CBF in the superior posterior cerebellum that were largely localized to bilateral Crus I and Crus II. Post hoc analyses showed that the changes were driven by a treatment-related decrease in CBF. Conclusions Fifteen minutes of high-frequency sub-threshold taVNS can induce sustained CBF decreases in the bilateral posterior cerebellum in a cohort of healthy subjects. This study lays the foundation for future studies in clinical popluations to assess whether similar effects can be observed and are related to treatment outcomes.
NOTCH Pathway Blockade Depletes CD133-Positive Glioblastoma Cells and Inhibits Growth of Tumor Neurospheres and Xenografts (2009)

Cancer stem cells (CSCs) are thought to be critical for the engraftment and long-term growth of many tumors, including glioblastoma (GBM). The cells are at least partially spared by traditional chemotherapies and radiation therapies, and finding new treatments that can target CSCs may be critical for improving patient survival. It has been shown that the NOTCH signaling pathway regulates normal stem cells in the brain, and that GBMs contain stem-like cells with higher NOTCH activity. We therefore used low-passage and established GBM-derived neurosphere cultures to examine the overall requirement for NOTCH activity, and also examined the effects on tumor cells expressing stem cell markers. NOTCH blockade by gamma-secretase inhibitors (GSIs) reduced neurosphere growth and clonogenicity in vitro, whereas expression of an active form of NOTCH2 increased tumor growth. The putative CSC markers CD133, NESTIN, BMI1, and OLIG2 were reduced following NOTCH blockade. When equal numbers of viable cells pretreated with either vehicle (dimethyl sulfoxide) or GSI were injected subcutaneously into nude mice, the former always formed tumors, whereas the latter did not. In vivo delivery of GSI by implantation of drug-impregnated polymer beads also effectively blocked tumor growth, and significantly prolonged survival, albeit in a relatively small cohort of animals. We found that NOTCH pathway inhibition appears to deplete stem-like cancer cells through reduced proliferation and increased apoptosis associated with decreased AKT and STAT3 phosphorylation. In summary, we demonstrate that NOTCH pathway blockade depletes stem-like cells in GBMs, suggesting that GSIs may be useful as chemotherapeutic reagents to target CSCs in malignant gliomas.
How to train your ViT? Data, Augmentation, and Regularization in Vision Transformers (2021)

Vision Transformers (ViT) have been shown to attain highly competitive performance for a wide range of vision applications, such as image classification, object detection and semantic image segmentation. In comparison to convolutional neural networks, the Vision Transformer's weaker inductive bias is generally found to cause an increased reliance on model regularization or data augmentation ("AugReg" for short) when training on smaller training datasets. We conduct a systematic empirical study in order to better understand the interplay between the amount of training data, AugReg, model size and compute budget. As one result of this study we find that the combination of increased compute and AugReg can yield models with the same performance as models trained on an order of magnitude more training data: we train ViT models of various sizes on the public ImageNet-21k dataset which either match or outperform their counterparts trained on the larger, but not publicly available JFT-300M dataset.
Regulation of the class II-associated invariant chain gene in normal and mutant B lymphocytes. (1990)

The invariant chain protein is intracellularly associated with class II major histocompatibility proteins. In many cases, the expression of these molecules appears to be regulated in a similar manner. Contained within the promoter of the invariant chain gene are sequences (X and I gamma 1) that are similar to the X and Y box elements of class II genes, suggesting that these sequences might be involved in its regulation. DNase I footprinting reveals additional cis-acting elements (I gamma 2 and I gamma 3) that contain sequence similarities to NF-kappa B and/or H2TF1/KBF1 recognition sequences. A series of fusion constructs with the chloramphenicol acetyltransferase reporter gene were used to analyze the role of these sequences (I gamma 1, I gamma 2, I gamma 3, and X and Y elements) in both normal and mutant B lymphocytes. These data suggest the likelihood of multiple X box proteins in B cells, which can act as both negative and positive regulatory factors.