gebhart/patrepeval huggingface dataset:
Profiles of Extracellular miRNA in Cerebrospinal Fluid and Serum from Patients with Alzheimer's and Parkinson's Diseases Correlate with Disease Status and Features of Pathology (2014)

The discovery and reliable detection of markers for neurodegenerative diseases have been complicated by the inaccessibility of the diseased tissue--such as the inability to biopsy or test tissue from the central nervous system directly. RNAs originating from hard to access tissues, such as neurons within the brain and spinal cord, have the potential to get to the periphery where they can be detected non-invasively. The formation and extracellular release of microvesicles and RNA binding proteins have been found to carry RNA from cells of the central nervous system to the periphery and protect the RNA from degradation. Extracellular miRNAs detectable in peripheral circulation can provide information about cellular changes associated with human health and disease. In order to associate miRNA signals present in cell-free peripheral biofluids with neurodegenerative disease status of patients with Alzheimer's and Parkinson's diseases, we assessed the miRNA content in cerebrospinal fluid and serum from postmortem subjects with full neuropathology evaluations. We profiled the miRNA content from 69 patients with Alzheimer's disease, 67 with Parkinson's disease and 78 neurologically normal controls using next generation small RNA sequencing (NGS). We report the average abundance of each detected miRNA in cerebrospinal fluid and in serum and describe 13 novel miRNAs that were identified. We correlated changes in miRNA expression with aspects of disease severity such as Braak stage, dementia status, plaque and tangle densities, and the presence and severity of Lewy body pathology. Many of the differentially expressed miRNAs detected in peripheral cell-free cerebrospinal fluid and serum were previously reported in the literature to be deregulated in brain tissue from patients with neurodegenerative disease. These data indicate that extracellular miRNAs detectable in the cerebrospinal fluid and serum are reflective of cell-based changes in pathology and can be used to assess disease progression and therapeutic efficacy.
Global Gene Expression Changes by Several Phytochemicals in Human Colorectal Cancer Cell (2011)

파이토케미칼은 식물유래의 비 영양 성분으로서 항염증, 항산화, 및 화학적 암 예방 등의 생리활성을 가지고 있는 물질이다. 본 연구에서, 우리는 다섯 가지의 다른 파이토케미칼(resveratrol, genistein, epicatechin gallate, diallyl disulfide, caffeic acid phenethyl ester)이 대장암 세포주의 성장과 유전자 발현에 미치는 영향을 연구하였다. 세포 생존율 연구결과, 처리한 ECG를 제외한 모든 파이토케미칼에 의해 농도의존적으로 세포생존율이 감소함을 확인하였다. 또한, oligo DNA microarray 실험을 통해 다섯 종류의 파이토케미칼에 의해 공통적으로 증가 되는 유전자 6개와 공통적으로 발현이 감소되는 유전자 7개를 선별하였다. 공통적으로 발현이 증가되는 유전자를 선택하여 RT-PCR 방법을 통해 발현을 증명하였다. 또한, 파이토케미칼에 의한 NAG-1 단백질의 발현 증가도 확인하였다. 이러한 연구결과는 파이토케미칼에 의해 중재되어 지는 화학적 암 예방법의 일반적인 분자 기전을 이해하는데 도움을 줄 것으로 생각된다. Phytochemicals, non-nutrient chemicals derived from plants, have been shown to have anti-inflammation, anti-oxidation, and chemopreventive effects. In the current study, we investigated whether five different phytochemicals (resveratrol, genistein, epicatechin gallate, diallyl disulfide, and caffeic acid phenethyl ester) alter cell growth and gene expression in human colorectal cancer HCT116 cells. Using a cell viability assay, we found that each of the phytochemicals tested inhibited HCT116 cell growth in a dose-dependent manner. Additionally, using human oligo DNA microarray analysis, we found that only six genes were commonly up-regulated and seven genes were commonly down-regulated in response to each phytochemical treatment. For the commonly up-regulated genes, the microarray analysis was confirmed by reverse transcription.PCR using gene-specific primers. In addition, NAG-1 protein was up-regulated by all treated phytochemcials. The results of this study may help to enhance our understanding of the general molecular mechanisms of chemoprevention that are mediated by phytochemicals in human colorectal cancer.
Diffraction imaging using shot and opening-angle gathers: A prestack time migration approach (2014)

ABSTRACT We have developed a migration scheme that can image weak diffractions in time. This significantly contributes to conventional interpretation in detecting small-scale faults and heterogeneities. The proposed scheme images diffractions using the shot and opening-angle gathers generated by prestack time migration (PSTM). Here, the shot and opening-angle gather represents a 2D migrated gather in terms of shot locations and opening angles between the incident- and scattered-rays. We muted the Fresnel zones related to reflections, corrected phases of diffractions, and enhanced diffractions in the migrated gathers. As a result, the proposed diffraction PSTM can image diffractions with and without phase-reversal. Moreover, the weak diffractions tangent to reflections can be clearly imaged. Diffraction PSTM can update migration velocities according to behaviors of reflection and diffraction events in the migrated gathers by scanning, thus overcoming a crucial problem in diffraction imaging. The reflector dips used in diffraction PSTM are obtained by picking the angles related to reflections in the shot and opening-angle gathers for a partial migration. Synthetic and field data tests demonstrate the validity of diffraction PSTM.
Pharmacokinetics of Morphine (1977)

The disposition of morphine in serum and that in the cerebral cortex during normocarbia and hypercarbia were determined in dogs. Normocarbia (pHa‘ 7.41; PaCO2 36 torr) was maintained by controlled ventilation. Hypercarbia (pHa’ 7.41; PaCO2 69 torr) was induced by inhalation of 10 per cent CO2, balan
Mechanics of oriented electrospun nanofibrous scaffolds for annulus fibrosus tissue engineering (2007)

Engineering a functional replacement for the annulus fibrosus (AF) of the intervertebral disc is contingent upon recapitulation of AF structure, composition, and mechanical properties. In this study, we propose a new paradigm for AF tissue engineering that focuses on the reconstitution of anatomic fiber architecture and uses constitutive modeling to evaluate construct function. A modified electrospinning technique was utilized to generate aligned nanofibrous polymer scaffolds for engineering the basic functional unit of the AF, a single lamella. Scaffolds were tested in uniaxial tension at multiple fiber orientations, demonstrating a nonlinear dependence of modulus on fiber angle that mimicked the nonlinearity and anisotropy of native AF. A homogenization model previously applied to native AF successfully described scaffold mechanical response, and parametric studies demonstrated that nonfibrillar matrix, along with fiber connectivity, are key contributors to tensile mechanics for engineered AF. We demonstrated that AF cells orient themselves along the aligned scaffolds and deposit matrix that contributes to construct mechanics under loading conditions relevant to the in vivo environment. The homogenization model was applied to cell-seeded constructs and provided quantitative measures for the evolution of matrix and interfibrillar interactions. Finally, the model demonstrated that at fiber angles of the AF (28 degrees -44 degrees ), engineered material behaved much like native tissue, suggesting that engineered constructs replicate the physiologic behavior of the single AF lamella. Constitutive modeling provides a powerful tool for analysis of engineered AF neo-tissue and native AF tissue alike, highlighting key mechanical design criteria for functional AF tissue engineering.
PATHOMECHANISMS IN CHANNELOPATHIES OF SKELETAL MUSCLE AND BRAIN (2006)

Ion channelopathies are a diverse array of human disorders caused by mutations in ion channel genes. This review focuses on the pathogenic mechanisms of channelopathies affecting skeletal muscle and brain arising from mutations of voltage-gated ion channels and fast ligand-gated ion channels expressed at the surface membrane. Derangements in channel function alter the electrical excitability of the cell and thereby increase susceptibility to transient symptomatic attacks including myasthenia, periodic paralysis, myotonic stiffness, seizures, headache, dyskinesia, or episodic ataxia. Although these disorders are rare, they stand out as exemplary cases for which disease pathogenesis can be traced from a point mutation to altered protein function, to altered cellular activity, and to clinical phenotype. The study of these disorders has provided insights on channel structure-function relations, the physiological roles of ion channels, and rational approaches toward therapeutic intervention for many disorders of cellular excitability.
A randomised study of peginterferon and ribavirin for 16 versus 24 weeks in patients with genotype 2 chronic hepatitis C (2006)

16 weeks and 24 weeks of peginterferon treatment with weight-based ribavirin at a dose of 1000-1200 mg/day provided equal efficacy in patients with HCV2 who achieved RVR at 4 weeks.
Visual Place Recognition with Repetitive Structures (2013)

Repeated structures such as building facades, fences or road markings often represent a significant challenge for place recognition. Repeated structures are notoriously hard for establishing correspondences using multi-view geometry. Even more importantly, they violate the feature independence assumed in the bag-of-visual-words representation which often leads to over-counting evidence and significant degradation of retrieval performance. In this work we show that repeated structures are not a nuisance but, when appropriately represented, they form an important distinguishing feature for many places. We describe a representation of repeated structures suitable for scalable retrieval. It is based on robust detection of repeated image structures and a simple modification of weights in the bag-of-visual-word model. Place recognition results are shown on datasets of street-level imagery from Pittsburgh and San Francisco demonstrating significant gains in recognition performance compared to the standard bag-of-visual-words baseline and more recently proposed burstiness weighting.
Wilms' tumor 1 susceptibility (WT1) gene products are selectively expressed in malignant mesothelioma. (1995)

The distinction between malignant mesothelioma and other neoplastic processes involving the pleura is difficult, partly due to the lack of specific markers expressed on mesothelioma. Because of evidence suggesting that the Wilms' tumor susceptibility gene (WT1), unlike other tumor suppressor genes, is restricted mostly to mesenchymally derived tissues, we hypothesized that the WT1 gene products could serve as a potential marker for mesothelioma. The expression of WT1 mRNA was analyzed in 19 malignant mesothelioma cell lines and 9 tumors and compared with the expression of WT1 in 10 non-small cell lung cancer lines and 9 lung cancer specimens. WT1 mRNA was detectable by Northern analysis in 16 of 19 mesothelioma cell lines and in 5 of 8 malignant mesothelioma tumors. In contrast, WT1 mRNA was not detected by Northern analysis in non-small cell lung cancer lines or carcinomas. Immunoprecipitation with an anti-WT1 monoclonal antibody showed that a 52- to 54-kd protein was present in 4 mesothelioma cell lines. Immunostaining with this antibody localized the WT1 protein to the nucleus in two mesothelioma lines and in 20 of 21 mesothelioma tumors examined. This distinctive pattern of nuclear immunoreactivity was absent in 26 non-mesothelioma tumors involving the lung, including 20 non-small cell lung carcinomas. The detection of WT1 mRNA or protein may thus provide a specific molecular or immunohistochemical marker for differentiation of mesothelioma from other pleural tumors, in particular, adenocarcinoma.
Systemic malignancies as a cause of unexpected microangiopathic hemolytic anemia and thrombocytopenia. (2011)

Tumor cells from malignancies of any type-carcinoma, sarcoma, lymphoma, leukemia-may cause systemic arteriolar and capillary obstructions. The high shear rates of blood passing through these obstructions result in fragmentation of the red cells and can cause severe anemia, described as microangiopathic hemolytic anemia (MAHA).The thrombi caused by these obstructions consume platelets and can lead to severe thrombocytopenia. MAHA (defined by fragmented red cells on the peripheral blood smear and evidence of hemolysis) and thrombocytopenia are the clinical features of syndromes described as thrombotic microangiopathies (TMAs). If a malignancy is not recognized as the cause of TMA, the diagnosis of thrombotic thrombocytopenic purpura (TTP) may be considered and plasma exchange, the essential treatment for TTP, may be initiated-a critical decision because this treatment carries a high risk of serious complications. This review describes the clinical features that should suggest a search for systemic malignancy as the cause of unexpected MAHA and thrombocytopenia. Recognition of a systemic malignancy is critical to the initiation of appropriate chemotherapy and avoidance of inappropriate use of plasma exchange treatment.
Upregulation of the Fas Receptor Death-Inducing Signaling Complex after Traumatic Brain Injury in Mice and Humans (2002)

Recent studies have implicated Fas in the pathogenesis of inflammatory, ischemic, and traumatic brain injury (TBI); however, a direct link between Fas activation and caspase-mediated cell death has not been established in injured brain. We detected Fas-Fas ligand binding and assembly of death-inducing signaling complexes (DISCs) [Fas, Fas-associated protein with death domain, and procaspase-8 or procaspase-10; receptor interacting protein (RIP)-RIP-associated interleukin-1beta converting enzyme and CED-3 homolog-1/Ced 3 homologous protein with a death domain-procaspase-2] by immunoprecipitation and immunoblotting within mouse parietal cortex after controlled cortical impact. At the time of DISC assembly, procaspase-8 was cleaved and the cleavage product appeared at 48 hr in terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling-positive neurons. Cleavage of caspase-8 was accompanied by caspase-3 processing detected at 48 hr by immunohistochemistry, and by caspase-specific cleavage of poly(ADP-ribose) polymerase at 12 hr. Fas pathways were also stimulated by TBI in human brain, because Fas expression plus Fas-procaspase-8 interaction were robust in contused cortical tissue samples surgically removed between 2 and 30 hr after injury. To address whether Fas functions as a death receptor in brain cells, cultured embryonic day 17 cortical neurons were transfected with an adenoviral vector containing the gene encoding Fas ligand. After 48 hr in culture, Fas ligand expression and Fas-procaspase-8 DISC assembly increased, and by 72 hr, cell death was pronounced. Cell death was decreased by approximately 50% after pan-caspase inhibition (Z-Val-ALa-Asp(Ome)-fluoromethylketone). These data suggest that Fas-associated DISCs assemble in neurons overexpressing Fas ligand as well as within mouse and human contused brain after TBI. Therefore, Fas may function as a death receptor after brain injury.
Assignment of Enzymatic Functions to Specific Regions of the PLP-Dependent Heme Protein Cystathionine β-Synthase (1999)

Cystathionine beta-synthase is a unique heme protein that catalyzes a pyridoxal phosphate (or PLP)-dependent beta-replacement reaction. The reaction involves the condensation of serine and homocysteine and constitutes one of the two major avenues for detoxification of homocysteine in mammals. The enzyme is allosterically regulated by S-adenosylmethionine (AdoMet). In this study, we have characterized the kinetic, spectroscopic, and ligand binding properties of a truncated catalytic core of cystathionine beta-synthase extending from residues 1 through 408 in which the C-terminal 143 residues have been deleted. This is similar to a natural variant of the protein that has been described in a homocystinuric patient in which the predicted peptide is 419 amino acids in length. Truncation leads to the formation of a dimeric enzyme in contrast to the tetrameric organization of the native enzyme. Some of the kinetic properties of the truncated enzyme are different from the full-length form, most notably, significantly higher K(m)s for the two substrates, and loss of activation by AdoMet. This is paralleled by the absence of AdoMet binding to the truncated form, whereas four AdoMet molecules bind cooperatively to the full-length tetrameric enzyme with a K(d) of 7. 4 microM. Steady-state kinetic analysis indicates that the order of substrate addition is important. Thus, preincubation of the enzyme with homocysteine leads to a 2-fold increase in V(max) relative to preincubation of the enzyme with serine. Since the intracellular concentration of serine is significantly greater than that of homocysteine, the physiological significance of this phenomenon needs to be considered. Based on ligand binding studies and homology searches with protein sequences in the database, we assign residues 68-209 as being important for PLP binding, residues 241-341 for heme binding, and residues 421-469 for AdoMet binding.
Induction of Tolerance in Macrophages by Cholera Toxin B Chain (1999)

Model systems of human type 1 diabetes have revealed an important role of cellular immune reactions involving macrophages and T cells in the destruction of autologous insulin-producing pancreatic beta cells. Recently, the cholera toxin B chain (CTB) was found to suppress T cell-dependent autoimmune diseases including autoimmune diabetes of nonobese diabetic mice. Therefore, we tested the hypothesis that CTB exerts much of its immunomodulatory activity by targeting macrophages. These studies are reviewed here. Cells of the human monocyte line Mono Mac 6 were exposed to CTB and subsequently tested for proinflammatory immunoreactivity in response to challenge with endotoxin (LPS from Escherichia coli, 10 ng/ml for 5 h). Incubation of monocytes with CTB (10 microgram/ml) suppressed a later proinflammatory response to LPS as demonstrated by suppression of TNFalpha release from 6.7 +/- 0.7 ng/ml in cultures without CTB preexposure to 1.8 +/- 1.1 ng/ml in CTB-pretreated cells (p < 0.001). In contrast, the release of IL-10 remained inducible after CTB pretreatment. RT-PCR analysis showed that the suppression of TNFalpha production occurred at the level of mRNA formation. Control experiments excluded a role of possible contamination of CTB by endotoxin or the intact cholera toxin. Tolerance induction was maximal after 5 h of CTB exposure and persisted for 24 h. The suppressive effect of CTB was dose-dependent and no more recognizable at </=1 microgram/ml. Incubation with IL-10- and TGFbeta-neutralizing antibodies during CTB pretreatment prevented tolerization of macrophages. IFNgamma (1,200 U/ml) was found to antagonize actions of CTB. In contrast to desensitization by low doses of LPS, tolerance induction by CTB occurred 'silently', i.e. in the absence of a measurable proinflammatory response. In view of the potent instructive role of the innate immune system on T cell responses these findings are important in understanding how CTB prevents the development of autoimmune diabetes and improves tolerance to islet autoantigens.
A stereoselective synthesis of indole-.beta.-N-glycosides: an application to the synthesis of rebeccamycin (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA stereoselective synthesis of indole-.beta.-N-glycosides: an application to the synthesis of rebeccamycinMichel Gallant, James T. Link, and Samuel J. DanishefskyCite this: J. Org. Chem. 1993, 58, 2, 343–349Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jo00054a015https://doi.org/10.1021/jo00054a015research-articleACS PublicationsRequest reuse permissionsArticle Views1016Altmetric-Citations107LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Cell-laden microengineered pullulan methacrylate hydrogels promote cell proliferation and 3D cluster formation (2011)

The ability to encapsulate cells in three-dimensional (3D) environments is potentially of benefit for tissue engineering and regenerative medicine. In this paper, we introduce pullulan methacrylate (PulMA) as a promising hydrogel platform for creating cell-laden microscale tissues. The hydration and mechanical properties of PulMA were demonstrated to be tunable through modulation of the degree of methacrylation and gel concentration. Cells encapsulated in PulMA exhibited excellent viability. Interestingly, while cells did not elongate in PulMA hydrogels, cells proliferated and organized into clusters, the size of which could be controlled by the hydrogel composition. By mixing with gelatin methacrylate (GelMA), the biological properties of PulMA could be enhanced as demonstrated by cells readily attaching to, proliferating, and elongating within the PulMA/GelMA composite hydrogels. These data suggest that PulMA hydrogels could be useful for creating complex, cell-responsive microtissues, especially for applications that require controlled cell clustering and proliferation.
Medium‐dose ultraviolet A1 phototherapy and mRNA expression of TSLP, TARC, IL‐5, and IL‐13 in acute skin lesions in atopic dermatitis (2015)

Expression levels of the mediators TSLP, TARC, IL-5, and IL-13 in AD are interrelated. Phototherapy with UVA1 improves SCORAD indices and increases expression of TARC but has no direct effects on the expression of other molecules. It is likely that UVA1 also interferes with or acts via intermediators on the link between IL-5 and IL-13.
Colloidal gold nanoparticles: a novel nanoparticle platform for developing multifunctional tumor‐targeted drug delivery vectors (2006)

Abstract Nanotechnology applied to biological problems represents an emerging field with the potential to offer extremely sensitive diagnostics and targeted cancer therapies. However, to achieve these goals, nanoparticle delivery systems must outwit the many barriers that are intrinsic to the body's defenses, as well as those that develop during the growth and progression of tumors. The science is advancing and, for example, true nanoscale tumor‐targeted drug delivery vectors are now able to reduce the likelihood of opsonization in the bloodstream and uptake by the reticuloendothelial system. Other advances hold promise for delivering multiple therapeutic agents to non‐homogeneous populations of cancer cells in solid tumors. We briefly summarize herein our attempts to build such multifunctional nanotherapeutics using colloidal gold nanoparticles. Specifically we discuss the development of colloidal gold‐based drugs that are designed to target the delivery of TNF and paclitaxel to solid tumors. Drug Dev. Res. 67:47–54, 2006. © 2006 Wiley‐Liss, Inc.
Mix Design of Mineral Mixture by Using EXCEL (2011)

矿质混合料组成设计的方法很多,有试算法、正规方程法、图解法等.由于正规方程法解算复杂,一般很少使用,但用EXCEL(电子表格)进行解算矩阵方程,则相对准确、快速,所以用例题求解的方式,进行了方程解算的介绍,使矿质混合料配合比设计简单化.