gebhart/patrepeval huggingface dataset:
LGA: a method for finding 3D similarities in protein structures (2003)

We present the LGA (Local-Global Alignment) method, designed to facilitate the comparison of protein structures or fragments of protein structures in sequence dependent and sequence independent modes. The LGA structure alignment program is available as an online service at http://PredictionCenter.llnl.gov/local/lga. Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed. LGA also allows the clustering of similar fragments of protein structures.
Phosphodiesterase-5 inhibitors in management of pulmonary hypertension: Safety, tolerability, and efficacy (2010)

Pulmonary arterial hypertension (PAH) is a progressive disease that causes severe disability and has no cure. Over the past 20 years, a variety of treatment options have evolved for the management of PAH. With an expanded therapeutic armamentarium come more complex decisions regarding treatment options. Agent selection depends upon several factors including efficacy, side effect profile, and cost, as well as convenience of administration. We have undertaken a review of phosphodiesterase-5 (PDE-5) inhibitors in PAH with a focus on efficacy and safety. A literature search was conducted using the Medline and Cochrane Central Register of Controlled Trials databases (1966-February 2010) for relevant randomized clinical studies. Overall, 10 studies met our inclusion criteria. Sildenafil was the most commonly studied agent, followed by tadalafil and vardenafil. Most trials found that the PDE-5 inhibitors significantly improved exercise capacity and lowered pulmonary pressures. However, there were conflicting results regarding these agents' impact on improving cardiac function and functional class. Overall, these medications were effective and well tolerated with a relatively benign side effect profile. The PDE-5 inhibitors are an important option in treating PAH. While most of the published clinical data involved sildenafil, the other PDE-5 inhibitors show promise as well. Further studies are needed to determine the optimal doses of this therapeutic drug class, as well as its effects as adjunctive therapy with other agents in PAH.
Complexity, fractals, disease time, and cancer (2004)

Despite many years of research, a method to precisely and quantitatively determine cancer disease state remains elusive. Current practice for characterizing solid tumors involves the use of varying systems of tumor grading and staging and thus leaves diagnosis and clinical staging dependent on the experience and skill of the physicians involved. Although numerous disease markers have been identified, no combination of them has yet been found that produces a quantifiable and reliable measure of disease state. Newly developed genomic markers and other measures based on the developing sciences of complexity offer promise that this situation may soon be changed for the better. In this paper, we examine the potential of two measures of complexity, fractal dimension and percolation, for use as components of a yet to be determined "disease time" vector that more accurately quantifies disease state. The measures are applied to a set of micrographs of progressive rat hepatoma and analyzed in terms of their correlation with cell differentiation, ratio of tumor weight to rat body weight and tumor growth time. The results provide some support for the idea that measures of complexity could be important elements of any future cancer "disease time" vector.
Metabolism of Prostaglandins in Diabetic Subjects (1985)

We evaluated the plasma levels of thromboxane B2 (Tx B2) and 6-keto PG F1α in both healthy controls and diabetic subjects before and after forearm ischemia, and the effects of trapidil on prostaglandin metabolism of these subjects. Our observations were listed as follows.(1) Before ischemia, plasma levels of Tx B2 and 6-keto PG F1α were 101.4±75.0pg/ml (Mean±SEM) and 115.1±14.6pg/ml in controls, and 181.4±161.4pg/ml and 65.2±9.0pg/ml in diabetics, respectively. In diabetics, plasma levels of 6-keto PG F1α was significantly lower than in controls (p<0.01).(2) After ischemia, plasma levels of Tx B2 and 6-keto PG F1α were 177.1±136.2pg/ml and 227.4±10.5pg/ml in diabetics, respectively. In diabetics, forearm ischemia did not induce the increase in plasma level of 6-keto PG F1α significantly, and was significantly lower than those in controls (p<0.05).(3) After trapidil treatment in diabetics, plasma levels of Tx B2 did not change significantly. Plasma levels of 6-keto PG F1α was 82.7±22.8pg/ml before ischemia, and 127.7±23.1pg/ml after ischemia. After ischemia, plasma levels of 6-keto PG F1α was significantly higher than those before treatment (p<0.01).The results indicate that the secretion of prostacyclin to forearm ischemia is decreased in diabetics. These abnormalities may play an important role in the pathogenesis and/or development of diabetic micro- and macro-angiopathy. Trapidil, known as coronary vasodilator, would be useful for its promoting effect of prostacyclin production, although further study would be needed to elucidate the detailed mechanisms.
Evaluation of Novel ECG Signal Processing on Quantification of Transient Ischemia and Baseline Wander Suppression (2007)

The performance assessment of a novel ECG signal processing technology in Fidelity 100 (test) and four modern ECG systems (controls) was conducted. A quantitative evaluation for one control and a test system was done by simultaneous recordings on 54 patients undergoing percutaneous coronary intervention (PCI) and on a biological reference signal from an ECG simulator. A qualitative performance of baseline wander suppression was done on all five systems. The results showed that the Fidelity 100 system provided excellent detection and quantification of transient ischemia and baseline wander suppression.
Morphological characterization of substance P receptor‐immunoreactive neurons in the rat spinal cord and trigeminal nucleus caudalis (1995)

Although there is considerable evidence that primary afferent-derived substance P contributes to the transmission of nociceptive messages at the spinal cord level, the population of neurons that expresses the substance P receptor, and thus are likely to respond to substance P, has not been completely characterized. To address this question, we used an antibody directed against the C-terminal portion of the rat substance P receptor to examine the cellular distribution of the receptor in spinal cord neurons. In a previous study, we reported that the substance P receptor decorates almost the entire dendritic and somatic surface of a subpopulation of spinal cord neurons. In the present study we have taken advantage of this labeling pattern to identify morphologically distinct subpopulations of substance P receptor-immunoreactive neurons throughout the rostral-caudal extent of the spinal cord. We observed a dense population of fusiform substance P receptor-immunoreactive neurons in lamina I at all segmental levels. Despite having the highest concentration of substance P terminals, the substantia gelatinosa (lamina II) contained almost no substance P receptor-immunoreactive neurons. Several distinct populations of substance P receptor-immunoreactive neurons were located in laminae III-V; many of these had a large, dorsally directed dendritic arbor that traversed the substantia gelatinosa to reach the marginal layer. Extensive labeling was also found in neurons of the intermediolateral cell column. In the ventral horn, we found that labeling was associated with clusters of motoneurons, notably those in Onuf's nucleus in the sacral spinal cord. Finally, we found no evidence that primary afferent fibers express the substance P receptor. These results indicate that relatively few, but morphologically distinct, subclasses of spinal cord neurons express the substance P receptor. The majority, but not all, of these neurons are located in regions that contain neurons that respond to noxious stimulation.
MHC matching fails to prevent long-term rejection of iPSC-derived neurons in non-human primates (2019)

Cell therapy products (CTP) derived from pluripotent stem cells (iPSCs) may constitute a renewable, specifically differentiated source of cells to potentially cure patients with neurodegenerative disorders. However, the immunogenicity of CTP remains a major issue for therapeutic approaches based on transplantation of non-autologous stem cell-derived neural grafts. Despite its considerable side-effects, long-term immunosuppression, appears indispensable to mitigate neuro-inflammation and prevent rejection of allogeneic CTP. Matching iPSC donors' and patients' HLA haplotypes has been proposed as a way to access CTP with enhanced immunological compatibility, ultimately reducing the need for immunosuppression. In the present work, we challenge this paradigm by grafting autologous, MHC-matched and mis-matched neuronal grafts in a primate model of Huntington's disease. Unlike previous reports in unlesioned hosts, we show that in the absence of immunosuppression MHC matching alone is insufficient to grant long-term survival of neuronal grafts in the lesioned brain.
Current treatment of ulcerative colitis. (2011)

Ulcerative colitis (UC) is a chronic disease featuring recurrent inflammation of the colonic mucosa. The goal of medical treatment is to rapidly induce a steroid-free remission while at the same time preventing complications of the disease itself and its treatment. The choice of treatment depends on severity, localization and the course of the disease. For proctitis, topical therapy with 5-aminosalicylic acid (5-ASA) compounds is used. More extensive or severe disease should be treated with oral and local 5-ASA compounds and corticosteroids to induce remission. Patients who do not respond to this treatment require hospitalization. Intravenous steroids or, when refractory, calcineurin inhibitors (cyclosporine, tacrolimus), tumor necrosis factor-α antibodies (infliximab) or immunomodulators (azathioprine, 6-mercaptopurine) are then called for. Indications for emergency surgery include refractory toxic megacolon, perforation, and continuous severe colorectal bleeding. Close collaboration between gastroenterologist and surgeon is mandatory in order not to delay surgical therapy when needed. This article is intended to give a general, practice-orientated overview of the key issues in ulcerative colitis treatment. Recommendations are based on published consensus guidelines derived from national and international guidelines on the treatment of ulcerative colitis.
The specificity of the syngeneic mixed leukocyte response, a primary anti-I region T cell proliferative response, is determined intrathymically. (1982)

In previous studies, the syngeneic MLR of peripheral T cells was shown to be predominantly an I region-restricted function. In this report we show that adult thymocytes are also capable of responding to syngeneic irradiated stimulator cells in a syngeneic MLR, provided that TCGF is added to the culture system. Using this assay, it was possible for the first time to examine the pattern of I region restriction within the thymus itself. Analysis of the thymocyte syngeneic MLR in thymuses from radiation-induced bone marrow chimeras demonstrated that the MHC preference seen in the peripheral T cell population also existed in cells resident within the thymus. Experiments utilizing congenitally athymic mice transplanted with allogeneic thymic grafts demonstrated that both peripheral T cells and thymocytes from such animals displayed a strong preferential proliferation toward stimulator cells bearing thymic-type MHC determinants. The results in the nude model thus demonstrate that the thymus by itself is sufficient to impart such restriction specificity on a developing T cell repertoire. These results are consistent with the notion that the thymus exerts selective pressure on maturing T cell populations that results in a skewing of the T cell repertoire toward the recognition of thymic-type I region products, and that this MHC preference exists before expansion of T cells in the periphery.
논문 : 금호강 유역 산림의 경관생태적 패턴분석 (2004)

산림의 단편화와 같은 인위적 교란은 유역생태계의 지속성에 영향을 미치기 때문에, 본 연구는 각종 개발사업에 따른 산림의 단편화를 사전에 예방하기 위해서 경관지수와 GIS를 이용하여 금호강 유역에 분포하는 산림구조를 정략화하였다. 소유역 단위의 경관지수값은 인자분석에 의해 전체분산을 또% 정도 설명하는 3개의 공통인자를 단순화하였다. 산림단편화 정도는 소유역별 인자점수를 토대로 계산하였고, 이는 도시지역 면적률(r=0.827, p<0.01, R2=0.685), 고도(r=-0.637, p<0.01)그리고 경사도(r=-0.593, p<0.01)와 상호관련성이 있는 것으로 나타났다. 이상과 같이 본 연구는 금호강 유역관리를 위한 산림경관의 건전성 및 구조적 패턴을 평가하기 위한 방법론과 경관지수값을 제시하였다. 향후에는 경관패턴 및 그 변화가 유역환경의 건전성에 미치는 영향을 규명하기 위한연구가 필요할 것이다.
Loss of RNA‐binding motif protein 3 expression is associated with right‐sided localization and poor prognosis in colorectal cancer (2015)

Our observations indicate that loss of RBM3 expression is an unfavourable prognostic marker in CRC, and is linked to right-sided tumour localization.
p53 isoforms regulate aging- and tumor-associated replicative senescence in T lymphocytes (2013)

Cellular senescence contributes to aging and decline in tissue function. p53 isoform switching regulates replicative senescence in cultured fibroblasts and is associated with tumor progression. Here, we found that the endogenous p53 isoforms Δ133p53 and p53β are physiological regulators of proliferation and senescence in human T lymphocytes in vivo. Peripheral blood CD8+ T lymphocytes collected from healthy donors displayed an age-dependent accumulation of senescent cells (CD28-CD57+) with decreased Δ133p53 and increased p53β expression. Human lung tumor-associated CD8+ T lymphocytes also harbored senescent cells. Cultured CD8+ blood T lymphocytes underwent replicative senescence that was associated with loss of CD28 and Δ133p53 protein. In poorly proliferative, Δ133p53-low CD8+CD28- cells, reconstituted expression of either Δ133p53 or CD28 upregulated endogenous expression of each other, which restored cell proliferation, extended replicative lifespan and rescued senescence phenotypes. Conversely, Δ133p53 knockdown or p53β overexpression in CD8+CD28+ cells inhibited cell proliferation and induced senescence. This study establishes a role for Δ133p53 and p53β in regulation of cellular proliferation and senescence in vivo. Furthermore, Δ133p53-induced restoration of cellular replicative potential may lead to a new therapeutic paradigm for treating immunosenescence disorders, including those associated with aging, cancer, autoimmune diseases, and HIV infection.
Constituents of the Essential Oil of Ethiopian Cymbopogon citratus Stapf (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConstituents of the Essential Oil of Ethiopian Cymbopogon citratus StapfBerhanu Abegaz, Paulos G. Yohannes, and R. Karl DieterCite this: J. Nat. Prod. 1983, 46, 3, 424–426Publication Date (Print):May 1, 1983Publication History Published online1 July 2004Published inissue 1 May 1983https://pubs.acs.org/doi/10.1021/np50027a022https://doi.org/10.1021/np50027a022research-articleACS PublicationsRequest reuse permissionsArticle Views345Altmetric-Citations47LEARN 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-Alertsclose Get e-Alerts
Bistability and Irregular Oscillations in Pairs of Opto-Thermal Micro-Oscillators (2023)

In this work, we experimentally and numerically investigate the nonlinear dynamics of pairs of coupled opto-thermal micro-oscillators. The oscillators are driven into limit cycle oscillations using an external constant power laser source and coupled via mechanical linkages. As the input laser power is increased, the oscillators transition from a state of synchrony to a state of bistability that manifests as irregular oscillations in the experiments. The experiments are performed on two sets of devices with different coupling strengths, which reveal that the laser power required for the transition to irregular oscillations increases with an increase in the coupling strength. A numerical parameter sweep in the coupling strength and laser power parameter space reveals a similar trend.
Mathematica Notebooks supporting "Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations" (2021)

Mathematica notebooks and data for journal article "Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations". The zip file contains two Mathematica notebooks (“Wolfram Mathematica 11/12”; www.wolfram.com) and excel files with data for the generation of the final domains for Fig 2 (glycolysis-case) and Fig 4 and 5 (cancer-case). In order to reproduce the calculations for these figures, the Mathematica notebook “DomainSolver.nb” is provided to solve the final domains and identify negative and positive signs starting from calculated control coefficients and initial values. This makes the procedure fully reproducible, permitting the generation of the final domains used in Fig 2 (glycolysis-case) and Figs 4 and 5 (cancer-case). The notebook contains an interactive script that requires to open two (glycolysis-case) or three (cancer-case) excel files (xlsx) with: 1) one matrix (glycolysis-case) or an ensemble of control-coefficient matrices (cancer-case); 2) list of initial domains (glycolysis-case and cancer-case); and 3) additional constraints for individual activities (only cancer-case, Eq (13) and (14)). Also, a second Mathematica notebook, “ControlSolver.nb”, is provided to generate the control coefficients by random sampling of metabolite elasticities for the cancer-case study. This notebook contains another interactive script that requires to open one (cancer-case) excel file (xlsx) with a description of the network structure, flux values, disequilibrium ratios, substrate/product competitive inhibitions (Substrate competitions), inhibitors, activators, and moiety conservations. Two documents are provided with the instructions for use.
Flat, Highly Connected Optical Network for Data Centers (2019)

A novel flat optical DC network approach using only low radix electrical switches and high data rate optical links is investigated. Compared to Clos, it provides resilience and ∼40% hardware savings with ∼60% higher throughput.
Preparation of WC-WB-W<SUB>2</SUB>B Composites from B<SUB>4</SUB>C-W-WC Powders and their Mechanical Properties (2002)

Sintered composites of WC–WB–W2B were prepared from B4C–W–WC powders using a reactive energization hot-pressing technique that initiated a solid state reaction between B4C and W. Below a WC mole fraction of 0.769 in the starting powder, WB and WC were formed according to the reaction B4C+5W+xWC=WB+(1+x)WC, while WB, W2B, and WC were produced above a mole fraction of 0.854. Densely sintered bodies were not obtained for pure WC. Composites of WC–WB–W2B obtained at WC mole fractions between 0.854 and 0.956 were fully consolidated, having high Young’s modulus and Vickers hardness values, and a fracture toughness which were comparable to those of WC.
Laboratory demonstration of IED detection using a high-flux neutron source (Conference Presentation) (2018)

Phoenix has demonstrated direct detection of buried explosive material by interrogation with an intense neutron source in a laboratory environment. The technique analyzes neutron-induced emission of characteristic gamma rays by each element, so it senses the explosive material itself. The high yield of the Phoenix neutron generator (up to 3x10^11 neutrons/second) represents a leap in detection times and standoff distances for neutron-based IED detection technology. Detection experiments ranged from standoff distances of up to 7 meters, which was the limit of the laboratory space. Simulants for nitrogen-based explosives were buried in sand of different moisture levels at depths of up to 28 cm (distance to top of explosive). The fast, high-resolution gamma-ray detector array is placed 50 cm above the suspect location. The method follows a concept of operations which assumes a selection of high-risk locations have been identified using ground-penetrating radar or satellite. The location is then scanned to determine the presence of explosives. The gamma radiation emitted due to the activation is analyzed to determine a presence of 10.8 MeV nitrogen gammas higher than background. The technique can also be used as a primary detection method. The measurements validate Monte Carlo modeling of neutron-based activation techniques. Example detection times: 1.4 seconds for 30-liter jug of TNT buried 8 cm in wet soil at a standoff of 5 m, or 37 seconds for 10-liter of TNT buried 30 cm in dry sand at a standoff of 10 m.
The structure of the copper/zinc oxide catalyst by an in-situ EXAFS study (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe structure of the copper/zinc oxide catalyst by an in-situ EXAFS studyKazuyuki Tohji, Yasuo Udagawa, Takanori Mizushima, and Akifumi UenoCite this: J. Phys. Chem. 1985, 89, 26, 5671–5676Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/j100272a019https://doi.org/10.1021/j100272a019research-articleACS PublicationsRequest reuse permissionsArticle Views988Altmetric-Citations86LEARN 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 options Get e-Alerts