gebhart/patrepeval huggingface dataset:
Analyzing Epistemic and Aleatoric Uncertainty for Drusen Segmentation in Optical Coherence Tomography Images (2021)

Age-related macular degeneration (AMD) is one of the leading causes of permanent vision loss in people aged over 60 years. Accurate segmentation of biomarkers such as drusen that points to the early stages of AMD is crucial in preventing further vision impairment. However, segmenting drusen is extremely challenging due to their varied sizes and appearances, low contrast and noise resemblance. Most existing literature, therefore, have focused on size estimation of drusen using classification, leaving the challenge of accurate segmentation less tackled. Additionally, obtaining the pixel-wise annotations is extremely costly and such labels can often be noisy, suffering from inter-observer and intra-observer variability. Quantification of uncertainty associated with segmentation tasks offers principled measures to inspect the segmentation output. Realizing its utility in identifying erroneous segmentation and the potential applications in clinical decision making, here we develop a U-Net based drusen segmentation model and quantify the segmentation uncertainty. We investigate epistemic and aleatoric uncertainty capturing model confidence and data uncertainty respectively. We present segmentation results and show how uncertainty can help formulate robust evaluation strategies. We visually inspect the pixel-wise uncertainty and segmentation results on test images. We finally analyze the correlation between segmentation uncertainty and accuracy. Our results demonstrate the utility of leveraging uncertainties in developing and explaining segmentation models for medical image analysis.
Low VT Mo(O,N) metal gate electrodes on HfSiON for sub-45nm pMOSFET Devices (2006)

We report band-edge pFET threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> ~ 0.28 V) for MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> on HfSiON gate dielectric using a standard high temperature gate first metal-inserted poly-stack (MIPS) process flow. We also report p-FETs V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> of 0.45 V using a MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /SiON gate stack, meeting the requirement for 45nm high-V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> CMOS technology. 30 % improvement in performance compared to our base-line poly-Si/SiON was observed by using both MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /SiON and MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> /HfSiON gate stacks. Excellent dielectric integrity is also shown for devices with MoO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> gated stack such as device mobility, NBTI and TDDB characteristics, as compared to our base-line poly/SiON devices
A novel fully human anti-NCL immunoRNase for triple-negative breast cancer therapy (2016)

Breast cancer is the most common cancer in women worldwide. A new promising anti-cancer therapy involves the use of monoclonal antibodies specific for target tumor-associated antigens (TAAs). A TAA of interest for immunotherapy of Triple Negative Breast Cancer (TNBC) is nucleolin (NCL), a multifunctional protein, selectively expressed on the surface of cancer cells, which regulates the biogenesis of specific microRNAs (miRNAs) involved in tumor development and drug-resistance. We previously isolated a novel human anti-NCL scFv, called 4LB5, that is endowed with selective anti-tumor effects. Here we report the construction and characterization of a novel immunoRNase constituted by 4LB5 and a human pancreatic RNase (HP-RNase) called "4LB5-HP-RNase". This immunoRNase retains both the enzymatic activity of human pancreatic RNase and the specific binding of the parental scFv to a panel of surface NCL-positive breast cancer cells. Notably, 4LB5-HP-RNase dramatically and selectively reduced the viability and proliferation of NCL-positive tumor cells in vitro and in vivo. Specifically, it induced apoptosis and reduced the levels of the tumorigenic miRNAs miR-21, -221 and -222. Thus, this novel immunoagent could be a valuable tool for the treatment of TNBC patients ineligible for currently available targeted treatments.
A global response to sulfur starvation inPseudomonas putidaand its relationship to the expression of low-sulfur-content proteins (2006)

Sulfur is essential for life on Earth, but its availability is limited in many environments. Here the sulfur-starvation response of the model soil bacterium Pseudomonas putida KT2440 is shown to be associated with an approximately fivefold reduction in the total soluble thiol content of the cell. A bioinformatic survey of the P. putida KT2440 genome identified 646 genes encoding proteins with a significantly lower than average sulfur content (low sulfur-content proteins, LSPs), the expression of which may have a role in the global reduction of cellular thiol content during sulfur starvation. Analysis of the genetic organization of the LSP-encoding genes showed that 31% were potentially transcriptionally associated with at least one other gene encoding a protein defined as an LSP. In particular, 55 LSP genes were located in three large clusters, termed low-sulfur islands (LSIs) here. The predicted identities of the proteins encoded by the LSIs strongly suggest that the LSIs have a role in acquiring sulfur from organic sulfur sources during sulfur starvation. This hypothesis was supported by transcription fusion studies on a limited number of LSP promoters under low-sulfur conditions. In a wider survey of bacterial species, LSIs were found to be more prevalent in free-living, Gram-negative bacteria than in Gram-positive or obligately intracellular bacteria.
Skin lesion classification using oblique-incidence diffuse reflectance spectroscopic imaging (2002)

We discuss the use of a noninvasive in vivo optical technique, diffuse reflectance spectroscopic imaging with oblique incidence, to distinguish between benign and cancer-prone skin lesions. Various image features were examined to classify the images from lesions into benign and cancerous categories. Two groups of lesions were processed separately: Group 1 includes keratoses, warts versus carcinomas; and group 2 includes common nevi versus dysplastic nevi. A region search algorithm was developed to extract both one- and two-dimensional spectral information. A bootstrap-based Bayes classifier was used for classification. A computer-assisted tool was then devised to act as an electronic second opinion to the dermatologist. Our approach generated only one false-positive misclassification out of 23 cases collected for group 1 and two misclassifications out of 34 cases collected for group 2 under the worst estimation condition.
A Methodology for the Design of Self-Optimizing, Decentralized Content-Caching Strategies (2015)

We consider the problem of efficient content delivery over networks in which individual nodes are equipped with content caching capabilities. We present a flexible methodology for the design of cooperative, decentralized caching strategies that can adapt to real-time changes in regional content popularity. This design methodology makes use of a recently proposed reduced consensus optimization scheme, in which a number of networked agents cooperate in locating the optimum of the sum of their individual, privately known objective functions. The outcome of the design is a set of dynamic update rules that stipulate how much and which portions of each content piece an individual network node ought to cache. In implementing these update rules, the nodes achieve a collectively optimal caching configuration through nearest-neighbor interactions and measurements of local content request rates only. Moreover, individual nodes need not be aware of the overall network topology or how many other nodes are on the network. The desired caching behavior is encoded in the design of individual nodes' costs and can incorporate a variety of network performance criteria. Using the proposed methodology, we develop a set of content-caching update rules designed to minimize the energy consumption of the network as a whole by dynamically trading off transport and caching energy costs in response to changes in content demand.
Computer Vision Methods for Registration: Mixing 3D Knowledge & 2D Correspondences for Accurate Image Composition (1998)

Colloque avec actes et comité de lecture.
Co-Expression Networks In Generation Of Induced Pluripotent Stem Cells (iPSCs) (P1.047) (2014)

OBJECTIVE: We seek to find novel genes and pathways in somatic cell reprogramming using network analysis.BACKGROUND: iPSCs can be generated from somatic cells by the ectopic expression of four reprogramming factors (RFs) (OCT4, SOX2, KLF4, and c-MYC). Reprogramming of somatic cells from patients with neurological disorder by using iPSC technology has offered unique opportunities to generate “disease models in a petri dish”. Transcriptome changes during the reprogramming process have been difficult to study due to technical reasons, including the inefficient nature of current reprogramming strategies and the necessity of feeder cells. DESIGN/METHODS: We developed an adenoviral vector, where four RFs are controlled by individual CMV promoters in a single cassette (Ad-GFP-SOcMK), which allow the coordinated expression of RFs in a cell for a transient period of time, synchronizing the reprogramming process without feeder cells. To identify transcriptome changes, we analyzed the expression profile using Agilent SurePrint G3 microarrays at 6-hour intervals for 72 hrs after Ad-GFP-SOcMK induction of IMR90 fibroblasts. The array dataset was analyzed using several bioinformatics tools including Weighted Gene Co-Expression Network analysis (WGCNA). RESULTS: After 3-4 days of post-transduction with Ad-GFP-SOcMK, cells formed embryonic stem (ES) cell-like colonies. Colonies showed ES cell morphology and met ES cell criteria. WGCNA identified sixteen large gene co-expression modules, each containing gene ontology categories involved in cell differentiation and development. The analysis also identified hub transcripts highly correlated with cell reprogramming, which interestingly included many long non-coding RNAs (lncRNAs). Transcription factor overrepresentation analysis identified transcription factor signatures (KLF4, SOX10) that may regulate some of these modules. CONCLUSIONS: The use of a novel reprogramming method, which enabled highly synchronized reprogramming, identified unique biological networks that are vital to our understanding of iPSC generation. These networks identified pathways, hub genes and transcription factors, which are candidates for follow-up studies.Study Supported by: This work was supported by Grants RO1NS33123 and RC4NS073009 from the National Institutes of Neurological Disorders and Stroke to SMP.
Carbon nanotube electrodes for effective interfacing with retinal tissue (2009)

We have investigated the use of carbon nanotube coated microelectrodes as an interface material for retinal recording and stimulation applications. Test devices were micro-fabricated and consisted of 60, 30 mum diameter electrodes at spacing of 200 mum. These electrodes were coated via chemical vapor deposition of carbon nanotubes, resulting in conducting, three dimensional surfaces with a high interfacial area. These attributes are important both for the quality of the cell-surface coupling as well as for electro-chemical interfacing efficiency. The entire chip was packaged to fit a commercial multielectrode recording and stimulation system. Electrical recordings of spontaneous spikes from whole-mount neonatal mouse retinas were consistently obtained minutes after retinas were placed over the electrodes, exhibiting typical bursting and propagating waves. Most importantly, the signals obtained with carbon nanotube electrodes have exceptionally high signal to noise ratio, reaching values as high as 75. Moreover, spikes are marked by a conspicuous gradual increase in amplitude recorded over a period of minutes to hours, suggesting improvement in cell-electrode coupling. This phenomenon is not observed in conventional commercial electrodes. Electrical stimulation using carbon nanotube electrodes was also achieved. We attribute the superior performances of the carbon nanotube electrodes to their three dimensional nature and the strong neuro-carbon nanotube affinity. The results presented here show the great potential of carbon nanotube electrodes for retinal interfacing applications. Specifically, our results demonstrate a route to achieve a reduction of the electrode down to few micrometers in order to achieve high efficacy local stimulation needed in retinal prosthetic devices.
Cross-Priming as a Predominant Mechanism for Inducing CD8+ T Cell Responses in Gene Gun DNA Immunization (2001)

DNA immunization induces CD8(+) CTL responses by bone marrow-derived APCs, which are directly transfected with a plasmid DNA and/or acquire Ags from DNA-transfected non-APCs. To investigate the relative contribution of DNA-transfected APCs vs non-APCs to the initiation of CD8(+) T cell responses, we used tissue-specific promoter-directed gene expression and adoptive transfer systems in gene gun DNA immunization. In this study, we demonstrated that non-APC-specific gene expressions induced significant CD8(+) CTL and IFN-gamma-producing cells and Ab responses, whereas APC-specific gene expressions led to moderate CTL and IFN-gamma-producers, but no Ab responses. Interestingly, mice immunized with a non-APC-specific plasmid induced more rapid, vigorous, and prolonged proliferation of adoptively transferred Ag-specific CD8(+) T cells than APC-specific plasmid-immunized mice. In addition, the in vivo proliferative responses elicited by a non-APC-specific plasmid administration were dependent on TAP, but were independent of CD4(+) T cell help. Collectively, our results suggest that cross-priming, in which Ags expressed in non-APCs are taken up, processed, and presented by APCs, plays an important role in the initiation, magnitude, and maintenance of CD8(+) T cell responses in gene gun DNA immunization.
Response to Letter Regarding Article, “Percutaneous Implantation of the CoreValve Self-Expanding Valve Prosthesis in High-Risk Patients With Aortic Valve Disease: The Siegburg First-in-Man Study” (2007)

We agree with Dr Grover and colleagues that on-pump surgical aortic valve replacement is currently the gold standard for operable patients with severe aortic valve stenosis. However, the need for general anesthesia, thoracotomy, and extracorporeal circulation results in a significant risk of morbidity and mortality, particularly in patients with numerous comorbid conditions.
The H-Density Ratio for Address Assignment Efficiency An Update on the H ratio (2001)

This document provides an update on the "H ratio" defined in RFC 1715. It defines a new ratio which the authors claim is easier to understand.
Polyphenols from Tamarix nilotica: LC–ESI-MSn Profiling and In Vivo Antifibrotic Activity (2018)

<i>Tamarix nilotica</i> (Ehrenb.) Bunge (Tamaricaceae), an indigenous plant to the Middle East region, is well-known as a medicinal plant for treating many human ailments. The current study aimed at exploring the polyphenol profile of the alcohol soluble fraction of aqueous <i>T. nilotica</i> extract, assessing its in vivo antifibrotic activity and the possible underlying mechanism, to unravel the impact of quantitative difference of sulphated polyphenols content on the antifibrotic activity of <i>T. nilotca</i> grown in two different habitats. Polyphenol profiling of <i>T. nilotica</i> extracts was performed using HPLC-HRESI-QTOF-MS-MS. The major polyphenol components included sulphated flavonoids, phenolic acids and free aglycones. The antifibrotic activity was evaluated through carbon tetrachloride-induced liver fibrosis in rats. Biochemical evaluations revealed that both fractions ameliorated the increased levels of hepatic aminotransferases, lipid peroxidation, hydroxyproline, α-smooth muscle actin (<i>α</i>-SMA), tumor necrosis factor-<i>α</i> (TNF-<i>α</i>), cyclooxygenase-2 (COX-2) and nuclear factor kappa B (NF-κB). Moreover, both fractions reduced catalase activity (CAT) and enhanced hepatic glutathione (GSH) content. Histopathological imaging undoubtedly confirmed such results. In conclusion, the <i>T. nilotica</i> polyphenol-rich fraction exhibited potential antifibrotic activity in rats. Significant alterations in GSH levels were recorded based on the sulphated polyphenol metabolite content.
Epithelial Barrier Function and Ultrastructure of Gelatinous Drop-like Corneal Dystrophy (2000)

The high epithelial permeability observed in GDLD corneas was directly correlated with abnormalities in epithelial structure, including irregular cell junctions. This suggests that the abnormal M1S1 gene product may affect epithelial cell junctions resulting in increased cell permeability in GDLD corneas.
Phase transformations in some hafnium-tantalum-titanium-zirconium alloys (1997)

Gastric bypass surgery may render an additional benefit of weight loss and improved healthy behavior for bariatric patients' family members.
Serendipitous formation of meso-free corroles in the [3+1] porphyrin and [3+2] sapphyrin syntheses (2022)

During the preparative investigation of [Formula: see text]-expanded porphyrinoids based on the retro-Diels-Alder reaction of bicyclo[2.2.2]octadiene(BCOD)-fused precursors for benzo- and benzo[[Formula: see text]]fluorantho[9,10]-[[Formula: see text]]porphyrins by the [3+1] porphyrin synthesis using tripyrrane-1,14-dicarbaldehyde and BCOD-fused pyrroles, serendipitous formation of the corresponding corroles was observed. After elucidation of the reaction conditions, the [3+1] reaction afforded 21,31-dihydro-21,31-ethanobenzo[[Formula: see text]]fluorantho[9,10-[Formula: see text]]corrole in 23% yield as well as a trace amount of the corresponding porphyrin. In the sapphyrin synthesis by the [3+2] approach using the tripyrrane-1,14-dicarbaldehyde and a bipyrrole, the similar reaction conditions resulted in the formation of 5-pyrrolylcorrole in a 38% yield as well as isosmaragdyrin and the originally targeted sapphyrin.
Telomere dynamics in monkeys: Increased cell turnover in macaques infected with chimeric simian‐human immunodeficiency viruses (1999)

To address the question of how cell turnover is affected by retroviral infections, we used the telomeric terminal restriction fragments (TRFs) as markers of cell replicative history and measured their length in macaques infected with chimeric simian-human immunodeficiency viruses (SHIVs). The TRF lengths of mononuclear cells in 104 samples, including longitudinal samples from nine cynomolgus and ten pig-tailed macaques infected with SHIV, and in samples from 26 uninfected macaques, were quantitated by an improved method, based on two-dimensional calibration of DNA sizes, pulsed field electrophoresis, and high-resolution Southern blot images. The average TRF lengths of peripheral blood mononuclear cells (PBMCs) from uninfected pig-tailed (14.9+/-1.6 kbp) and cynomolgus (14.1+/-1.8 kbp) macaques were about 3 and 5 kbp longer than those of human infants and 30-year-old adults, respectively. The rate of TRF length shortening in infected pig-tailed macaques was significantly (P = 0.035) higher (2.2-fold) than in uninfected monkeys. The TRFs in SHIV-infected cynomolgus monkeys, which, in general, had lower viral loads than pig-tailed macaques, shortened on average more rapidly (1.6-fold) than in uninfected animals, but the difference was not statistically significant. The TRFs of mononuclear cells from the lymph nodes of two rapidly progressing SHIV-infected macaques that developed AIDS and died also shortened in parallel but somewhat more rapidly than in the PBMCs. These results suggest that the rate of PBMC turnover in macaques could be increased several-fold during infections by immunodeficiency viruses, likely due to immune activation by SHIV antigens.
Complexing Methylene Blue with Phosphorus Dendrimers to Increase Photodynamic Activity (2017)

The efficiency of photodynamic therapy is limited mainly due to low selectivity, unfavorable biodistribution of photosensitizers, and long-lasting skin sensitivity to light. However, drug delivery systems based on nanoparticles may overcome the limitations mentioned above. Among others, dendrimers are particularly attractive as carriers, because of their globular architecture and high loading capacity. The goal of the study was to check whether an anionic phosphorus dendrimer is suitable as a carrier of a photosensitizer-methylene blue (MB). As a biological model, basal cell carcinoma cell lines were used. We checked the influence of the MB complexation on its singlet oxygen production ability using a commercial fluorescence probe. Next, cellular uptake, phototoxicity, reactive oxygen species (ROS) generation, and cell death were investigated. The MB-anionic dendrimer complex (MB-1an) was found to generate less singlet oxygen; however, the complex showed higher cellular uptake and phototoxicity against basal cell carcinoma cell lines, which was accompanied with enhanced ROS production. Owing to the obtained results, we conclude that the photodynamic activity of MB complexed with an anionic dendrimer is higher than free MB against basal cell carcinoma cell lines.
Effects of Multiple Dosing of Epinephrine on Aqueous Humor Dynamics in Human Eyes (2002)

Numerous studies have provided conflicting evidence to explain the ocular hypotensive mechanism of action of epinephrine. Although epinephrine has been shown consistently to increase outflow facility, its effects on aqueous flow and uveoscleral outflow are not as clear. The purpose of this study was to clarify the effects of multiple doses of topical epinephrine on aqueous humor dynamics in human eyes. This was done by evaluating the four main parameters that determine steady state intraocular pressure. These parameters were assessed at baseline and after a week of twice-daily treatment of epinephrine hydrochloride 2% to one eye. Twenty-six human volunteers were enrolled in the study. Intraocular pressure was measured by pneumatonometry, aqueous flow and trabecular outflow facility by fluorophotometry, episcleral venous pressure by venomanometry and uveoscleral outflow by mathematical calculation. In epinephrine-treated eyes compared to baseline, intraocular pressure and aqueous flow were reduced from 21.2 +/- 0.3 to 17.1 +/- 0.2 mmHg (19%, p = .01) and 3.3 +/- 0.2 to 2.9 +/- 0.2 microl/min (12%, p = .03), respectively. Trabecular outflow facility obtained by fluorophotometry was increased from 0.18 +/- 0.02 to 0.26 +/- 0.03 microl/min/mmHg (44%, p = .02). Topical epinephrine did not significantly affect uveoscleral outflow or episcleral venous pressure. In conclusion, multiple topical doses of epinephrine lowered intraocular pressure in human volunteers by reducing aqueous humor formation and increasing trabecular outflow facility. The increase in uveoscleral outflow suggested by other studies was not observed.