gebhart/patrepeval huggingface dataset:
Segmentation of the endocardial wall of the left atrium using local region-based active contours and statistical shape learning (2010)

Atrial fibrillation, a cardiac arrhythmia characterized by unsynchronized electrical activity in the atrial chambers of the heart, is a rapidly growing problem in modern societies. One treatment, referred to as catheter ablation, targets specific parts of the left atrium for radio frequency ablation using an intracardiac catheter. Magnetic resonance imaging has been used for both pre- and and post-ablation assessment of the atrial wall. Magnetic resonance imaging can aid in selecting the right candidate for the ablation procedure and assessing post-ablation scar formations. Image processing techniques can be used for automatic segmentation of the atrial wall, which facilitates an accurate statistical assessment of the region. As a first step towards the general solution to the computer-assisted segmentation of the left atrial wall, in this paper we use shape learning and shape-based image segmentation to identify the endocardial wall of the left atrium in the delayed-enhancement magnetic resonance images.
Microcosm TNG: a framework for distributed open hypermedia (2000)

Increased amounts of information and users' rising demands for advanced link services pose strong challenges to distributed hypermedia systems. Novel presentation facilities, nontextual digital media, personalization of content and structures, and many more techniques often require complex processing and thus imply new interaction styles. Microcosm TNG (The Next Generation), which is a framework for distributed open hypermedia, offers new mechanisms for desktop and Internet integration. It also promotes a modular approach to authoring hypermedia resources.
ONC201 Shows Potent Anticancer Activity Against Medullary Thyroid Cancer via Transcriptional Inhibition of RET, VEGFR2, and IGFBP2 (2021)

Gain-of-function point mutations in the receptor tyrosine kinase <i>RET</i>, a driver oncogene in medullary thyroid carcinoma (MTC), prevent apoptosis through inhibition of ATF4, a critical transcriptional regulator of endoplasmic reticulum stress. However, the critical regulatory mechanisms driving RET-dependent oncogenesis remain elusive, and there is a clinical need to identify a transcriptional RET inhibitor. Here, we found that RET depletion decreased <i>IGFBP2</i> and <i>VEGFR2</i> mRNA and protein expression in MTC cells. IGFBP2 knockdown decreased cell survival and migration of MTC cells. In patients, IGFBP2 expression increased in metastatic MTC, and high IGFBP2 associated with poor overall survival. VEGFR2 protein levels were positively associated with RET expression in primary tumors, and VEGF-mediated increased cell viability was RET dependent. The small-molecule ONC201 treatment of MTC cells caused apoptotic cell death, decreased transcription of RET, VEGFR2, IGFBP2, increased mRNA levels of <i>ATF4</i>, and ATF4 target genes including <i>DDIT3, BBC3, DUSP8, MKNK2, KLF9, LZTFL1</i>, and <i>SESN2</i> Moreover, IGFBP2 depletion increased ONC201-induced cell death. ONC201 inhibited tumor growth at a well-tolerated dose of 120 mg/kg/week administered by oral gavage and decreased MTC xenograft cell proliferation and angiogenesis. The protein levels of RET, IGFBP2, and VEGFR2 were decreased in ONC201-treated xenografts. Our study uncovered a novel ONC201 mechanism of action through regulation of RET and its targets, VEGFR2 and IGFBP2; this mechanism could be translated into the clinic and represent a promising strategy for the treatment of all patients with MTC, including those with TKI-refractory disease and other cancer with RET abnormalities.
An improved HLLE method for hypersonic viscous flows (2001)

Dissipation mechanisms of Godunov-type schemes are presented in the framework of unified representation. We first examined the causes of inaccuracy at the contact discontinuity and the dissipation mechanism in the numerical mass flux of the HLLEM scheme. Through a linear perturbation analysis on the oddeven decoupling problem, we discuss necessary conditions for designing a shock stable scheme. The curing methods for each specified problem are also presented. A new improved HLLE(HLLE+) scheme is proposed and analyzed on its dissipation mechanism. The diffusivity of the Godunov-type schemes is examined by computing two-dimensional hypersonic viscous flow. It is shown that the present method can accurately predict the surface heating rates without grid dependency.
No Downlink Pilots Are Needed in TDD Massive MIMO (2017)

We consider the Massive Multiple-Input Multiple-Output downlink with maximum-ratio and zero-forcing processing and time-division duplex operation. To decode, the users must know their instantaneous effective channel gain. Conventionally, it is assumed that by virtue of channel hardening, this instantaneous gain is close to its average and hence that users can rely on knowledge of that average (also known as statistical channel information). However, in some propagation environments, such as keyhole channels, channel hardening does not hold. We propose a blind algorithm to estimate the effective channel gain at each user, that does not require any downlink pilots. We derive a capacity lower bound of each user for our proposed scheme, applicable to any propagation channel. Compared with the case of no downlink pilots (relying on channel hardening), and compared with training-based estimation using downlink pilots, our blind algorithm performs significantly better. The difference is especially pronounced in environments that do not offer channel hardening.
Supplementary Figure 5 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells (2023)

Supplementary Figure 5 from NPM-ALK Oncogenic Tyrosine Kinase Controls T-Cell Identity by Transcriptional Regulation and Epigenetic Silencing in Lymphoma Cells
Imaging with THz OSCAT spectrometer (2011)

We present a novel THz imaging system based on an all-fiber THz-OSCAT spectrometer. First THz-OSCAT images are presented and properties of the system, as well its limitations are extensively discussed.
Finding Specification Pages from the Web (2006)

This paper presents a method of finding a specification page on the Web for a given object (e.g., ``Ch. d'Yquem'') and its class label (e.g., ``wine''). A specification page for an object is a Web page which gives concise attribute-value information about the object (e.g., ``county''-``Sauternes'') in well formatted structures. A simple unsupervised method using layout and symbolic decoration cues was applied to a large number of the Web pages to acquire candidate attributes for each class (e.g., ``county'' for a class ``wine''). We then filter out irrelevant words from the putative attributes through an author-aware scoring function that we called site frequency. We used the acquired attributes to select a representative specification page for a given object from the Web pages retrieved by a normal search engine. Experimental results revealed that our system greatly outperformed the normal search engine in terms of this specification retrieval.
An adaptive fuzzy evidential nearest neighbor formulation for classifying remote sensing images (2005)

The paper presents a novel adaptive fuzzy evidential nearest neighbor formulation for classifying remotely sensed images. The formulation combines the generalized fuzzy version of the Dempster-Shafer evidence theory (DSET) and the K-nearest neighbor (KNN) algorithm. Each of the K nearest neighbors provides evidence on the belongingness of the input pattern to be classified, and it is evaluated based on a measure of disapproval to achieve the adaptive capability during the classification process. The disapproval measure quantifies the lack of support with respect to the belongingness of the input pattern to a given class. Pieces of evidence are ranked based on their degree of disapproval and fused in a sequential manner. The pignistic Shannon entropy is used to estimate the degree of consensus among pieces of evidence provided by nearest neighbors and as a criterion for terminating the evidence fusion process. The paper reports the results of experimental work conducted to evaluate the proposed classification scheme using real multichannel remote sensing images. As will be demonstrated using the experimental results, the proposed classification scheme demonstrated robust performance and outperformed commonly used methods such as the K-nearest neighbor algorithm of Cover and Hart (1967), the fuzzy K-nearest neighbor algorithm of Keller et al. (1985), the evidence-theoretic K-nearest neighbor algorithm of Denoex (1995), and its fuzzy version of Zouhal and Denoex (1997). The performance of these techniques is examined with respect to the K-parameter and classification accuracy.
Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis (2015)

Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2-3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2-3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems.
Comparison of a fifth dose of a five-component acellular or a whole cell pertussis vaccine in children four to six years of age (1999)

A regimen consisting of five doses of a five-component acellular pertussis combination vaccine is safe and immunogenic in pre-school children. Local adverse reactions are common but are less painful and activity-limiting than a regimen of five doses of a whole cell pertussis vaccine.
Origins and development of biomedical engineering within chemical engineering (2004)

Abstract Over the past 45 years, the field of biomedical engineering has found a welcome home in academic chemical engineering departments and in companies working with artificial organs, medical devices, and pharmaceutical formulations. The contributions of chemical engineers to the definition and the growth of the field have been important and at times seminal. The development and early contributions in the biomedical field with special emphasis on the contributions of chemical engineers is examined. © 2004 American Institute of Chemical Engineers AIChE J , 50: 536–546, 2004
Stable Synthetic Bacteriochlorins for Photodynamic Therapy: Role of Dicyano Peripheral Groups, Central Metal Substitution (2H, Zn, Pd), and Cremophor EL Delivery (2012)

A series of four stable synthetic bacteriochlorins was tested in vitro in HeLa cells for their potential in photodynamic therapy (PDT). The parent bacteriochlorin (BC), dicyano derivative (NC)(2)BC and corresponding zinc chelate (NC)(2)BC-Zn and palladium chelate (NC)(2)BC-Pd were studied. Direct dilution of a solution of bacteriochlorin in an organic solvent (N,N-dimethylacetamide) into serum-containing medium was compared with the dilution of bacteriochlorin in Cremophor EL (CrEL; polyoxyethylene glycerol triricinoleate) micelles into the same medium. CrEL generally reduced aggregation (as indicated by absorption and fluorescence) and increased activity up to tenfold (depending on bacteriochlorin), although it decreased cellular uptake. The order of PDT activity against HeLa human cancer cells after 24 h incubation and illumination with 10 J cm(-2) of near-infrared (NIR) light is (NC)(2)BC-Pd (LD(50)=25 nM) > (NC)(2)BC > (NC)(2)BC-Zn ≈ BC. Subcellular localization was determined to be in the endoplasmic reticulum, mitochondria and lysosomes, depending on the bacteriochlorin. (NC)(2)BC-Pd showed PDT-mediated damage to mitochondria and lysosomes, and the greatest production of hydroxyl radicals as determined using a hydroxyphenylfluorescein probe. The incorporation of cyano substituents provides an excellent motif for the enhancement of the photoactivity and photostability of bacteriochlorins as PDT photosensitizers.
An Approach to the Use of Clinical Limits for Quality Control (1989)

An approach is proposed to adapt control procedures for the detection of clinically significant errors. It is based on a version of the predictive value theory (Bayes' Theorem) as applied to quantitative data. Examples are given for two situations, one in which the analytical performance exceeds the medical needs (glucose) and onein which the analytical performance does not meet the medical needs (calicum).
Synthesis of Nanocrystalline B2 Structured (Ru, Ir) Al in the Ternary Ru–Al–Ir System by Mechanical Alloying and its Thermal Stability (2001)

Abstract B2 structured single-phase (Ru,Ir)Al is synthesized directly in the ternary Ru– Al– Ir system by mechanical alloying. Complete solubility between pseudo-binary RuAl – IrAl is achieved in a composition range 10–25 at.% Ir, while the range for Al remains at 50 at.%. B2 structured (Ru, Ir) Al is formed by an abrupt reaction at the beginning of milling of all three compositions and a certain quantity of Ir was found to remain after the reaction. Further alloying and a reaction between Ir and sticking Al on the surfaces of milling tools take a much longer time and finally result in single phase B2 structured (Ru, Ir) Al. The ternary alloying element Ir has been found to ameliorate the sluggish reactivity of Ru by promoting the abrupt reaction. No decomposition process has been observed for the as-milled single-phase (Ru, Ir) Al by means of high-temperature X-ray diffraction, demonstrating the complete mutual solubility between pseudo-binary RuAl and IrAl in the present composition range. The structural evolution of as-milled materials includes reordering, strain relaxation and grain growth. The grain size of the as-milled (Ru, Ir) Al after exposure to elevated temperatures (up to 1273 K), turns out to be less than 30 nm and reflects its strong thermal stability.
8-Tetrahydropyran-2-yl Chromans: Highly Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors (2014)

A series of 2,3,4,4a,10,10a-hexahydropyrano[3,2-b]chromene analogs was developed that demonstrated high selectivity (>2000-fold) for BACE1 vs Cathepsin D (CatD). Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Guided by structure based design, changes to P2' and P3 moieties were explored. A conformationally restricted P2' methyl group provided inhibitors with excellent cell potency (37-137 nM) and selectivity (435 to >2000-fold) for BACE1 vs CatD. These efforts lead to compound 59, which demonstrated a 69% reduction in rat CSF Aβ1-40 at 60 mg/kg (PO).
Symmetrical Impedance Study on Inactivation Induced Degradation of Lithium Electrodes for Batteries Beyond Lithium-Ion (2014)

The degradation of the lithium (Li) electrode was investigated based on its structural transformation due to the inactivation of deposited Li using a Copper/LiNi1/3Mn1/3Co1/3O2 (NMC) cell and a Li | Li symmetrical cell. Depletion of active Li turned out to be the major reason for the failure of the Li electrode under our experimental conditions. Following the first charging (Li-deposition) of the Copper/NMC cell, the discharge process only recovered 23% of the total deposited Li back to the NMC cathode. Electrochemical impedance spectroscopy (EIS) experiments of the Li | Li symmetric cell demonstrated that the repeated inactivation during the deposition process leads to the growth of the deposited Li layer thereby forming three interfacial structures most likely originating from (i) residual Li | liquid electrolyte, (ii) cycled Li in the inner deposited Li layer | liquid electrolyte, and (iii) cycled Li on the outer deposited Li layer | liquid electrolyte. The voltage profile and EIS of the symmetric cell could be correlated with the degradation behavior exhibited by the Li electrode.
Dependable, efficient, scalable architecture for management of large-scale batteries (2010)

Conventional battery management systems (BMSs) for electric vehicles (EVs) are designed in an ad hoc way, causing the supply of EVs to fall behind the market demand. A well-designed and combined hardware-software architecture is essential for the management of a large-scale battery pack that consists of thousands of battery cells as in Tesla Motors and GM Chevy Volt. We propose a Dependable, Efficient, Scalable Architecture (DESA) that effectively monitors a large number of battery cells, efficiently controls and reconfigures, if needed, their connection arrangement. DESA is monarchy-based and supports hierarchical, autonomous management of battery cells, where a global BMS orchestrates a group of local BMSs. A local controller on each local BMS autonomously manages an array of battery cells, and the global controller reconfigures the connectivity of such battery-cell arrays in coordination with the local controllers. Configuration of a battery system is controlled by three types of switch---called P-, S-, and B-switches---and an algorithm that changes the setting of these switches. Our evaluation results show that DESA effectively tolerates battery-cell failures by order of magnitude---while achieving service cost savings 7.4 times---more than a conventional BMS. This superior performance not only extends the battery life signifcantly, but also provides the flexibility in supporting diverse electric power demands from a growing number of on-board applications.
Multimodal Graph-Theoretic Approach for Segmentation of the Internal Limiting Membrane at the Optic Nerve Head (2015)

In this work, we present a multimodal multiresolution graph-based method to segment the top surface of the retina called the internal limiting membrane (ILM) within optic-nerve-head-centered spectral-domain optical coherence tomography (SD-OCT) volumes. Having a precise ILM surface is crucial as this surface is utilized for measuring several structural parameters such as Bruch’s membrane opening-minimum rim width (BMO-MRW) and cup volume. The proposed method addresses the common current segmentation errors due to the presence of retinal blood vessels, deep cupping, or a very steep slope of the ILM. In order to resolve these issues, the volume is resampled using a set of gradient vector flow (GVF) based columns. The GVF field is computed according to an initial surface segmentation which is obtained through a multiresolution framework. The retinal blood vessel information (obtained from corresponding registered fundus photographs) along with shape prior information are incorporated in a graph-theoretic approach to compute the ILM segmentation. The method is tested on the SD-OCT volumes from 44 glaucoma subjects and significantly smaller errors were obtained than that from current approaches.
Analysis of dust samples from the Middle East using high-density resequencing micro-array RPM-TEI (2010)

A previously developed resequencing microarray, "Tropical and Emerging Infections (RPM-TEI v.1.0 chip)", designed to identify and discriminate between tropical diseases and other potential biothreat agents, their near-neighbor species, and/or potential confounders, was used to characterize the microbes present in the silt/clay fraction of surface soils and airborne dust collected from the Middle East. Local populations and U.S. military personnel deployed to the Middle East are regularly subjected to high levels of airborne desert dust containing a significant fraction of inhalable particles and some portion require clinical aid. Not all of the clinical symptoms can be directly attributed to the physical action of material in the human respiratory tract. To better understand the potential health effects of the airborne dust, the composition of the microbial communities associated with surface soil and/or airborne dust (air filter) samples from 19 different sites in Iraq and Kuwait was identified using RPM-TEI v.1.0. Results indicated that several microorganisms including a class of rapidly growing <i>Mycobacterium, Bacillus, Brucella, Clostridium</i> and <i>Coxiella burnetti</i>, were present in the samples. The presence of these organisms in the surface soils and the inhalable fraction of airborne dust analyzed may pose a human health risk and warrants further investigation. Better understanding of the factors influencing the composition of these microbial communities is important to address questions related to human health and is critical to achieving Force Health Protection for the Warfighter operating in the Middle East, Afghanistan, North Africa and other arid regions.
Phosphatidylinositol 3-kinase is necessary and sufficient for insulin-stimulated stress fiber breakdown. (1996)

Rat-1 fibroblasts overexpressing the human insulin receptor undergo rapid actin rearrangement in response to insulin. Breakdown of stress fibers present in quiescent cells is followed by transient membrane ruffling and a return of stress fibers. We investigated the signaling pathways that mediate this insulin-stimulated reorganization of the actin cytoskeleton, which was visualized with rhodamine-phalloidin. Treatment of cells with the phosphatidylinositol 3-kinase (PI3-kinase) inhibitor wortmannin prevented insulin action at the preliminary step of stress fiber breakdown. Cellular microinjection of a polyclonal antibody directed against the p85 subunit of PI3-kinase as well as a purified recombinant p85-SH2 domain protein also inhibited actin reorganization. Transient expression of a constitutively active form of PI3-kinase (p110*) was sufficient to cause both stress fiber breakdown and membrane ruffling in the absence of insulin. Microinjection of a polyclonal anti-Shc antibody or dominant negative N17-Ras protein did not affect actin dynamics, and although constitutively active V12-Ras caused modest cytoskeletal reorganization, this effect was blocked by pretreatment with wortmannin. In summary, activation of PI3-kinase is necessary and sufficient to stimulate actin rearrangement, indicating that PI3-kinase may initiate the only signaling cascade required for insulin to induce cytoskeletal restructuring.
Suppression of temperature dependence in EDFA gain by hybrid concatenation of antimony-doped silica EDF (2003)

Sb-doped silica EDF showed an opposite temperature dependent gain coefficients compared to Al-doped silica EDFs. Concatenation of two EDFs resulted in a gain variation less than /spl plusmn/0.25 dB for the saturated gain over 15 dB, within -40 to +80 /spl deg/C.