gebhart/patrepeval huggingface dataset:
INDEPENDENT COMPONENT ANALYSIS OF BIOMEDICAL SIGNALS (2000)

Biomedical signals from many sources including hearts, brains and endocrine systems pose a challenge to researchers who may have to separate weak signals arriving from multiple sources contaminated with artifacts and noise. The analysis of these signals is important both for research and for medical diagnosis and treatment. The applications of Independent Component Analysis (ICA) to biomedical signals is a rapidly expanding area of research and many groups are now actively engaged in exploring the potential of blind signal separation and signal deconvolution for revealing new information about the brain and body. In this review, we survey some recent applications of ICA to a variety of electrical, magnetic and hemodynamic measurements, drawing primarily from our own research. 1. INTRODUCTION The goal of this review is to provide an overview of recent applications of ICA to biomedical signal processing, with a focus on recordings from the brain. Because it is often difficult to interp...
Ultrasound image deconvolution using adaptive inverse filtering (2003)

Clinical ultrasound image quality typically suffers from reduced resolution due to the effects of limited effective aperture size (convolutional blurring), out-of-focus blurring and noise. Speckle noise in ultrasound images can be especially troublesome and significantly deteriorates image quality. This paper discusses the use of a novel approach developed for optical microscope images and applied to ultrasound. In earlier research, 3D microscope images were successfully deconvolved using an adaptive, least-mean-square solution to a statistical Wiener filter. The filter can be applied to two and three-dimensional images as a finite impulse response (FIR) filter solved adaptively using an inverse model of the point-spread-function (PSF). For ultrasound, the filter can be solved using the response to a phantom where the desired result is known a priori. The filter is solved adaptively to minimize the mean-square-error. The resulting filter can then be applied to any image acquired with the same transducer array and instrument parameters. The application of this type of filter to ultrasound is in the preliminary stages with some partial success obtained so far. Preliminary results are shown on phantom and clinical ultrasound data (courtesy of Diasonics, Inc.) processed by this method. The results are promising for improving resolution and minimizing noise.
Rat-brain Na,K-ATPase beta-chain gene: primary structure, tissue-specific expression, and amplification in ouabain-resistant HeLa C+ cells. (1986)

We deduced the complete amino acid sequence of the rat brain Na,K-ATPase beta-subunit from cDNA. The rat brain beta-subunit exhibits a high degree of primary sequence and secondary structural homology with the human and Torpedo beta-subunit polypeptides. Analysis of rat tissue RNA reveals that the beta-subunit gene encodes four separate mRNA species which are expressed in a tissue-specific fashion. In ouabain-resistant HeLa C+ cells, beta-subunit DNA sequences are amplified (approximately 20-fold) and beta-subunit mRNAs are overproduced relative to levels in parental HeLa cells. These results suggest that the beta-subunit plays an important role in Na,K-ATPase structure-function and in the mechanism underlying cellular resistance to the cardiac glycosides.
Register renaming and dynamic speculation: an alternative approach (1993)

Presents a novel mechanism that implements register renaming, dynamic speculation and precise interrupts. Renaming of registers is performed during the instruction fetch stage instead of the decode stage, and the mechanism is designed to operate in parallel with the tag match logic used by most cache designs. It is estimated that the critical path of the mechanism requires approximately the same number of logic levels as the tag match logic, and therefore should not impact cycle time. >
China,Science and Humanities (2001)

Mankind is today indeed at a turning point of history: For the first time, we recognize and experience the limitations set by the finite resources of the globe. But also for the first time in history, we truely have the capability to develop all the technological tools necessary to shape our future.
Steam explosion and its combinatorial pretreatment refining technology of plant biomass to bio‐based products (2015)

Pretreatment is a key unit operation affecting the refinery efficiency of plant biomass. However, the poor efficiency of pretreatment and the lack of basic theory are the main challenges to the industrial implementation of the plant biomass refinery. The purpose of this work is to review steam explosion and its combinatorial pretreatment as a means of overcoming the intrinsic characteristics of plant biomass, including recalcitrance, heterogeneity, multi-composition, and diversity. The main advantages of the selective use of steam explosion and other combinatorial pretreatments across the diversity of raw materials are introduced. Combinatorial pretreatment integrated with other unit operations is proposed as a means to exploit the high-efficiency production of bio-based products from plant biomass. Finally, several pilot- and demonstration-scale operations of the plant biomass refinery are described. Based on the principle of selective function and structure fractionation, and multi-level and directional composition conversion, an integrated process with the combinatorial pretreatments of steam explosion and other pretreatments as the core should be feasible and conform to the plant biomass refinery concept. Combinatorial pretreatments of steam explosion and other pretreatments should be further exploited based on the type and intrinsic characteristics of the plant biomass used, the bio-based products to be made, and the complementarity of the processes.
Allogenic donor splenocytes pretreated with antisense peptide against B7 prolong cardiac allograft survival (2004)

The interaction of T cell CD28/CTLA-4 receptors with B7 on antigen-presenting cells (APCs) represents an important co-stimulatory pathway in T cell activation or anergy. Our previous study indicated that recipients immunized with allogenic donor immature dendritic cells (DCs) or resting B cells could induce specific immune tolerance and prolong allograft survival. A possible mechanism for this observation is that the expression of B7 molecules is either at a low level or lacking on these cells. The present study investigates whether blockade of B7 molecules on donor splenocytes with a B7 antisense peptide (B7AP), i.e. a peptide analogue of the CD28-binding region, could induce specific immune tolerance and prolong allograft survival in the recipients. Both the lymphocyte proliferation reaction and the mice pinna cardiac allograft experiment were performed to evaluate the role of B7AP in inducing specific immune tolerance in recipients in vitro and in vivo. The results showed that 56.65% and 20.52% of C57BL/6 splenocytes expressed B7.1 and B7.2 molecules, respectively, on their cell surface. There were no significant changes of the B7 expression on such splenocytes after being treated by the B7AP (53.28% and 19.06%, respectively). B7AP inhibited the mixed lymphocyte reaction by up to 38.4% and a dose-response correlation was observed for inhibition. The recipients (BALB/c) immunized with B7AP-pretreated C57BL/6 splenocytes induced a specific immune hypo-response (43%versus control) and notably prolonged survival of the C57BL/6 cardiac allograft by up to 20.3 days. In contrast to the normal saline group (average: 8.6 days) and FTD(10) control peptide group (<4 days), the cardiac allograft survival of the test group was extended for an additional 11.7 days. These results strongly support the notion that immunization with donor splenocytes, which had been pretreated with B7AP, induced specific immune tolerance and prolonged allograft survival in the recipients.
Enantioselective Hydrogenation of β-Ketophosphonates with Chiral Ru(II) Catalysts (2012)

Highly effective asymmetric hydrogenation of β-ketophosphonates in the presence of Ru-(S)-SunPhos as catalyst was realized; good to excellent enantioselectivities (up to 99.9% ee) and excellent diastereoselectivities (96:4) were obtained.
A New Synergized Glutaraldehyde-Phenate Sterilizing Solution and Concentrated Disinfectant (1981)

Research leading to the development of Sporicidin, a new (synergized glutaraldehyde-phenate) sterilant and concentrated disinfectant, is reported. Microbial evaluation and shelf life testing of the new formulation was done using AOAC tests--Use-Dilution, Sporicidal, Tuberculocidal--and the E.P.A. Virucidal Test. Full-strength Sporicidin sterilizes (is sporicidal) in 6 3/4 hours at both 20C and 25C, and disinfects in 1-2 minutes. When diluted with 15 parts of tap water, Sporicidin is tuberculocidal, virucidal, and germicidal in 10 minutes, qualifying as a hospital disinfectant that will not "yellow" the hands or skin. The shelf life of activated Sporidicin, full strength or diluted 1 in 16, is 30 days. According to the data presented, which were the basis of E.P.A. registrations, Sporicidin is: (a) the fastest glutaraldehyde sterilant at room temperature, and (b) the only glutaraldehyde product that can be diluted below 2% and still qualify as a hospital disinfectant.
The Refinement Effect of Foreign Word Transliteration Query on Meta Search (2008)

문서에서 외래어가 일관되게 사용되지 않고 여러 이형태로 사용되고 있기 때문에, 정확한 질의어 일치를 지원하는 검색 시스템에서 외래어 질의로 문서를 검색하는데 어려움이 많다. 본 논문에서는 하나의 외래어로 질의할 경우, 원 질의어와 같은 뜻의 다양한 이형태 외래어 질의로 자동 확장하고 정제하여 더 많은 관련 문서를 손쉽게 검색할 수 있는 메타 검색 방법을 제안한다. 이 방법은 1차로 원 질의어에서 다양한 외래어 이형태를 통계적 방법으로 확장하고, 2차로 그 결과를 각 검색 엔진에게 질의하여 일정 개수 이상의 질의어가 문서에 나타났는지, 원 질의어의 문맥과 유사한 문맥에서 그 질의어가 쓰였는지를 비교하여, 같은 뜻의 유효한 외래어를 판별해 내고 이를 이용하여 검색할 수 있도록 한다. 실험 결과, 기준점으로 쓰인 1차로 만든 이형태로 검색했을 때 F값은 평균 38%이었으나, 제안된 방법인 2차로 정제된 질의어로 검색했을 때의 F값은 평균 81%로 매우 향상된 결과를 보였다. Foreign word transliterations are not consistently used in documents, which hinders retrieving some important relevant documents in exact term matching information retrieval systems. In this paper, a meta search method is proposed, which expands and refines relevant variant queries from an original input foreign word transliteration query to retrieve the more relevant documents. The method firstly expands a transliteration query to the variants using a statistical method. Secondly the method selects the valid variants: it queries each variant to the retrieval systems beforehand and checks the validity of each variant by counting the number of appearance of the variant in the retrieved document and calculating the similarity of the context of the variant. Experiment result showed that querying with the variants produced at the first step, which is a base method of the test, performed 38% in average F measure, and querying with the refined variants at the second step, which is a proposed method, significantly improved the performance to 81% in average F measure.
Anti-Toxin Antibodies in Prophylaxis and Treatment of Inhalation Anthrax (2009)

The CDC recommend 60 days of oral antibiotics combined with a three-dose series of the anthrax vaccine for prophylaxis after potential exposure to aerosolized Bacillus anthracis spores. The anthrax vaccine is currently not licensed for anthrax postexposure prophylaxis and has to be made available under an Investigational New Drug protocol. Postexposure prophylaxis based on antibiotics can be problematic in cases where the use of antibiotics is contraindicated. Furthermore, there is a concern that an exposure could involve antibiotic-resistant strains of B. anthracis. Availability of alternate treatment modalities that are effective in prophylaxis of inhalation anthrax is therefore highly desirable. A major research focus toward this end has been on passive immunization using polyclonal and monoclonal antibodies against B. anthracis toxin components. Since 2001, significant progress has been made in isolation and commercial development of monoclonal and polyclonal antibodies that function as potent neutralizers of anthrax lethal toxin in both a prophylactic and therapeutic setting. Several new products have completed Phase I clinical trials and are slated for addition to the National Strategic Stockpile. These rapid advances were possible because of major funding made available by the US government through programs such as Bioshield and the Biomedical Advanced Research and Development Authority. Continued government funding is critical to support the development of a robust biodefense industry.
Free-space microwave focusing by a negative-index gradient lens (2006)

Metamaterial structures designed to have simultaneously negative permittivity and permeability are known as left-handed materials. Their complexity and our understanding of their properties have advanced rapidly to the point where direct applications are now viable. We present a radial gradient-index lens with an index of refraction ranging from −2.67 (edge) to −0.97 (center). Experimentally, we find that the lens can produce field intensities at the focus that are greater than that of the incident plane wave. These results are obtained at 10.3GHz and in excellent agreement with full-wave simulations. We also demonstrate an advanced fabrication technique using conventional printed circuit board technology which offers significant design, mechanical, and cost advantages over other microwave lens constructions.
Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa (2010)

A novel Fe regulated bHLH transcription factor (OsIRO3) that plays an important role for Fe homeostasis in rice was identified. The inhibitory effect of OsIRO3 over-expression on Fe deficiency response gene expression combined with hypersensitivity of OsIRO3 over-expression lines to low Fe suggest that OsIRO3 is a negative regulator of the Fe deficiency response in rice.
Optimization algorithm for restoring an all-focused micromechanical structure image (2004)

This paper presents an optimization algorithm of a technique that generates an all-focused image from several differently focused images. The targeted characteristic of differently focused images is that each has only some in-focus regions and the rest of the image is out-of-focus. Using a sharpness function to defect the focused areas causes errors due to the fact that the out-of-focus objects are bigger than their actual size. Therefore, detection of feature edges is spatially incorrect. In addition, focused areas with low contrast cannot be easily distinguished from the out-of-focus regions. Recently we proposed a method to overcome these difficulties. The input images are first enhanced and then divided into different block sizes. The focused blocks are defined using a gradient function followed by a threshold and then a voting algorithm determines the best-focused pixels. Here, an optimization algorithm has been developed which speeds up the image restoration process by 57%.
DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm (2014)

The mantled floral phenotype of oil palm (Elaeis guineensis) affects somatic embryogenesis-derived individuals and is morphologically similar to mutants defective in the B-class MADS-box genes. This somaclonal variation has been previously demonstrated to be associated to a significant deficit in genome-wide DNA methylation. In order to elucidate the possible role of DNA methylation in the transcriptional regulation of EgDEF1, the APETALA3 ortholog of oil palm, we studied this epigenetic mark within the gene in parallel with transcript accumulation in both normal and mantled developing inflorescences. We also examined the methylation and expression of two neighboring retrotransposons that might interfere with EgDEF1 regulation. We show that the EgDEF1 gene is essentially unmethylated and that its methylation pattern does not change with the floral phenotype whereas expression is dramatically different, ruling out a direct implication of DNA methylation in the regulation of this gene. Also, we find that both the gypsy element inserted within an intron of the EgDEF1 gene and the copia element located upstream from the promoter are heavily methylated and show little or no expression. Interestingly, we identify a shorter, alternative transcript produced by EgDEF1 and characterize its accumulation with respect to its full-length counterpart. We demonstrate that, depending on the floral phenotype, the respective proportions of these two transcripts change differently during inflorescence development. We discuss the possible phenotypical consequences of this alternative splicing and the new questions it raises in the search for the molecular mechanisms underlying the mantled phenotype in the oil palm.
The Role of Human Leukocyte Antigen Matching in the Development of Multiethnic “Haplobank” of Induced Pluripotent Stem Cell Lines (2011)

Among the tools of regenerative medicine, induced pluripotent stem cells (iPSCs) are interesting because the donor genotype can be selected. The construction of banks of iPSC cell lines selected from human leukocyte antigen (HLA) homozygous donors has been proposed to be an effective way to match a maximal number of patients receiving cell therapy from iPSC lines. However, what effort would be required to constitute such a bank for a worldwide application has remained unexplored. We developed a probabilistic model to compute the number of donors to screen for constituting banks of best-chosen iPSC lines with homozygous HLA haplotypes (haplobanks) in four ancestry backgrounds. We estimated what percentage of the patients would be provided with single HLA haplotype matched cell lines. Genetic diversity leads to different outcomes for the four sets in all terms. A bank comprising iPSC lines representing the 20 most frequent haplotypes in each population would request quite different number of donors to screen, between 26,000 for European Americans and 110,000 for African Americans. It would also match different fractions of the recipient population, namely, more than 50% of the European Americans and 22% of African Americans. Conversely, a bank comprising the 100 iPSC lines with the most frequent HLA in each population would leave out only 22% of the European Americans, but 37% of the Asians, 48% of the Hispanics, and 55% of the African Americans. The constitution of a haplobank of iPSC lines is achievable through a large-scale concerted worldwide collaboration.
A new family of very long chain alpha,omega-dicarboxylic acids is a major structural fatty acyl component of the membrane lipids of Thermoanaerobacter ethanolicus 39E. (1994)

A new family of alpha,omega-dicarboxylic, very long chain fatty acids was isolated and characterized from the lipids of thermophilic anaerobic eubacterium, Thermoanaerobacter ethanolicus 39E. After the isolation of the membrane, the fatty acyl components were converted to methyl esters by acid-catalyzed methanolysis. The esterified fatty acyl components were purified by a variety of chromatographic techniques and analyzed by gas chromatography (GC) and GC-mass spectrometry (MS). One of the isolated, esterified alpha,omega-dicarboxylic, very long chain fatty acids was characterized by mass spectrometry, 1H and 13C NMR spectroscopy and Fourier transform infrared spectroscopy. NMR experiments used included double quantum filtered correlated spectroscopy (DQF-COSY) to establish spin connectivities and polarization transfer (DEPT) to measure the multiplicity of carbon signals split by protons. Based on these results, the structures of the other components could be deduced from their mass spectra. The new family of very long chain fatty acid methyl esters are alpha,omega-13,16-dimethylheptacosanedioate dimethyl ester (C29), alpha,omega-13,16-dimethyloctacosanedioate dimethyl ester (C30), alpha,omega-13,16-dimethylnonacosanedioate dimethyl ester (C31), and alpha,omega-13,16-dimethyltriacotanedioate dimethyl ester (C32). This family of fatty acids make up about 40% of fatty acyl components of the membrane of Thermoanaerobacter ethanolicus 39E. Almost all (> 90%) of the very long chain, alpha,omega-dicarboxylic fatty acid was alpha,omega-13,16-dimethyloctacosanedioic acid. A careful analysis of the structures of the alpha,omega-dicarboxylic acid strongly implies that the synthetic mechanism for formation is by tail-to-tail (omega)coupling of regular iso-branched fatty acids across opposite sides of the membrane.
Omecamtiv mecarbil: a new cardiac myosin activator for the treatment of heart failure (2015)

Results of phase I and phase II studies demonstrate that omecamtiv mecarbil is safe and well tolerated both as an intravenous and oral formulation. In healthy volunteers and chronic systolic heart failure patients, administration of omecamtiv mecarbil resulted in a concentration-dependent increase of left ventricular ejection time, ejection fraction, fractional shortening, and stroke volume. The first results of a double-blind, randomized, placebo-controlled phase IIb dose-finding study with the oral formulation of omecamtiv mecarbil demonstrated beneficial effects on cardiac function and N-terminal pro-brain natriuretic peptide levels. This study will provide essential dosing information for the requisite phase III trials which will investigate whether the beneficial effects of omecamtiv mecarbil translate into improved clinical outcomes.
Increased Levels of Keratin 16 Alter Epithelialization Potential of Mouse Skin Keratinocytes In Vivo and Ex Vivo (2001)

The process of wound repair in adult skin is complex, involving dermal contraction and epithelial migration to repair the lesion and restore the skin's barrier properties. At the wound edge, keratinocytes undergo many changes that engender an epithelialization behavior. The type II keratin 6 and type I keratins 16 and 17 are induced well before cell migration begins, but the role of these proteins is not understood. Forced expression of human K16 in skin epithelia of transgenic mice has been shown to cause dose-dependent skin lesions concomitant with alterations in keratin filament organization and in cell adhesion. Here we show, with the use of a quantitative assay, that these transgenic mice show a delay in the closure of full-thickness skin wounds in situ compared with wild-type and low-expressing K16 transgenic mice. We adapted and validated an ex vivo skin explant culture system to better assess epithelialization in a wound-like environment. Transgenic K16 explants exhibit a significant reduction of keratinocyte outgrowth in this setting. This delay is transgene dose-dependent, and is more severe when K16 is expressed in mitotic compared with post-mitotic keratinocytes. Various lines of evidence suggest that the mechanism(s) involved is complex and not strictly cell autonomous. These findings have important implications for the function of K16 in vivo.
Safety of targeting ROR1 for cancer immunotherapy with chimeric antigen receptor-modified T cells in a primate model (2014)

Meeting abstracts Immunotherapy with T cells expressing chimeric antigen receptors (CARs) specific for a tumor cell-surface molecule is effective for CD19+ B cell malignancies. There is interest in extending CAR-T cell therapy to epithelial tumors, which requires identifying molecules that can be