gebhart/patrepeval huggingface dataset:
Combined nested reverse transcription-PCR assay for prostate-specific antigen and prostate-specific membrane antigen in detecting circulating prostatic cells. (1997)

Accurate staging is an important issue in managing patients with prostate cancer. Current staging modalities are poor predictors for locally advanced disease. In the present study, we investigated the role of a peripheral blood-based, nested reverse transcription-PCR (RT-PCR) for prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSM) in prostate cancer staging. Our nested RT-PCR could detect both PSA and PSM mRNA in one LNCaP cell diluted in 10(6) mononuclear cells. None of the controls, including patients with benign prostate hyperplasia, normal male subjects, and female subjects, were positive for either marker, confirming the assay's specificity for prostate cancer. In patients with bony metastases, 100% were positive by combined PSA/PSM assays (64% by PSA and 91% by PSM). In patients with clinically localized prostate cancer, 29% were positive by combined PSA/PSM assays (13% by PSA and 23% by PSM). The combined PSA/PSM assay is more sensitive than the PSA assay alone in detecting circulating prostatic cells (P = 0.0071). PSM is a more sensitive marker than PSA (P = 0.042). We also correlated preoperative nested RT-PCR results with pathological findings in prostatectomy patients. Nested RT-PCR for PSA/PSM has an odds ratio of 20 in predicting tumor extracapsular penetration (P = 0.017). These results indicate that a nested RT-PCR result may provide the staging information unavailable from other modalities, including the clinical stage, initial serum PSA, and Gleason score. Additional investigation is needed to determine the ultimate role of this assay in the management of patients with prostate cancer.
Impact of Prior Treatment on the Efficacy of Adoptive Transfer of Tumor-Infiltrating Lymphocytes in Patients with Metastatic Melanoma (2021)

Patients previously treated with PD-1 or MAPK inhibition are significantly less likely to develop durable objective responses to ACT-TIL. While ACT-TIL is currently being investigated for treatment-refractory patients, it should also be considered as an initial treatment option for eligible patients with metastatic melanoma. See related commentary by Sznol, p. 5156.
Physiological Functions of APP Family Proteins (2011)

Biochemical and genetic evidence establishes a central role of the amyloid precursor protein (APP) in Alzheimer disease (AD) pathogenesis. Biochemically, deposition of the β-amyloid (Aβ) peptides produced from proteolytic processing of APP forms the defining pathological hallmark of AD; genetically, both point mutations and duplications of wild-type APP are linked to a subset of early onset of familial AD (FAD) and cerebral amyloid angiopathy. As such, the biological functions of APP and its processing products have been the subject of intense investigation, and the past 20+ years of research have met with both excitement and challenges. This article will review the current understanding of the physiological functions of APP in the context of APP family members.
Lactate Provocation of Panic Attacks (1984)

To assess the pharmacologic and phenomenologic comparability of lactate-induced and naturally occurring panic attacks, patients meeting DSM-III criteria for panic disorder or agoraphobia with panic attacks were infused with 0.5M racemic sodium lactate before and after successful drug treatment. Lactate-induced and naturally occurring panic attacks were symptomatically similar. Following treatment, the patients' response to lactate did not differ from that of normal controls, whereas the pretreatment panic rate was much higher. These data suggest that lactate acts, by as yet unidentified mechanisms, to trigger the same panic attacks as occur spontaneously in vulnerable persons.
Optical coherence tomography of cell dynamics in three-dimensional tissue models (2006)

Three-dimensional cell-based tissue models have been increasingly useful in the fields of tissue engineering, drug discovery, and cell biology. While techniques for building these tissue models have been advanced, there have been increasing demands for imaging techniques that are capable of assessing complex dynamic three-dimensional cell behavior in real-time and at larger depths in highly-scattering scaffolds. Understanding these cell behaviors requires advanced imaging tools to progress from characterizing two-dimensional cell cultures to complex, highly-scattering, thick three-dimensional tissue constructs. Optical coherence tomography (OCT) is an emerging biomedical imaging technique that can perform cellular-resolution imaging in situ and in real-time. In this study, we demonstrate that it is possible to use OCT to evaluate dynamic cell behavior and function in a quantitative fashion in four dimensions (three-dimensional space plus time). We investigated and characterized in thick tissue models a variety of cell processes, such as chemotaxis migration, proliferation, de-adhesion, and cell-material interactions. This optical imaging technique was developed and utilized in order to gain new insights into how chemical and/or mechanical microenvironments influence cellular dynamics in multiple dimensions. With deep imaging penetration and increased spatial and temporal resolution in three-dimensional space, OCT will be a useful tool for improving our understanding of complex biological interactions at the cellular level.
Functional analysis of the Tat trans activator of human immunodeficiency virus type 2 (1989)

The trans-activator (Tat) proteins of the related but distinct type 1 and type 2 human immunodeficiency viruses (HIV-1 and HIV-2) display incomplete functional reciprocity. One possible explanation of this observation, suggested by computer analysis of potential RNA secondary structures within the viral trans-activation response (TAR) elements, is that HIV-2 Tat requires the presentation of two viral RNA stem-loop sequences for full activity whereas HIV-1 Tat is maximally active upon presentation of a single stem-loop structure. Here, we demonstrate that the HIV-2 long terminal repeat indeed contains two functionally independent TAR elements. However, the second (3') TAR element of HIV-2 is significantly less active than the 5' TAR element and is functionally masked in the context of an intact HIV-2 long terminal repeat. Evidence is presented suggesting that the activities of these two HIV-2 TAR elements reflect, at least in part, their relative distances from the site of transcription initiation. Although the HIV-2 TAR element proximal to the viral mRNA cap site appears to be sufficient for effective trans activation by HIV-2 Tat in vitro, this functional redundancy may nevertheless serve to enhance HIV-2 replication in infected cells in vivo.
Over‐expression of cytosolic glutamine synthetase increases photosynthesis and growth at low nitrogen concentrations (2001)

Nitrogen, which is a major limiting nutrient for plant growth, is assimilated as ammonium by the concerted action of glutamine synthetase (GS) and glutamate synthase (GOGAT). GS catalyses the critical incorporation of inorganic ammonium into the amino acid glutamine. Two types of GS isozymes, located in the cytosol (GS1) and in the chloroplast (GS2) have been identified in plants. Tobacco (Nicotiana tabacum) transformants, over-expressing GS1 driven by the constitutive CaMV 35S promoter were analysed. GS in leaves of GS-5 and GS-8 plants was up-regulated, at the level of RNA and proteins. These transgenic plants had six times higher leaf GS activity than controls. Under optimum nitrogen fertilization conditions there was no effect of GS over-expression on photosynthesis or growth. However, under nitrogen starvation the GS transgenics had c. 70% higher shoot and c. 100% greater root dry weight as well as 50% more leaf area than low nitrogen controls. This was achieved by the maintenance of photosynthesis at rates indistinguishable from plants under high nitrogen, while photosynthesis in control plants was inhibited by 40-50% by nitrogen deprivation. It was demonstrated that manipulation of GS activity has the potential to maintain crop photosynthetic productivity while reducing nitrogen fertilization and the concomitant pollution.
In situ measurement of residual oil saturation (1976)

The accurate determination of residual oil saturation is of critical importance in evaluating the feasibility of applying an enhanced recovery process in a specific reservoir. Several methods have been used to estimate the residual oil saturation remaining in a reservoir near the end of a waterflood; these are the material balance calculation, waterflood calculations based on relative permeability data, and the analysis of saturations in as-received conventional cores. These methods provide merely an approximation of the amount of remaining oil, but results from these methods can sometimes be correlated with more accurate direct measurement techniques to evaluate the overall distribution of oil remaining in place. This study briefly summarizes several procedures for determining residual oil saturation and, as pertinent, outlines the advantages and limitations of each technique. The single-well tracer method is described in more detail in terms of 2 recent field applications. (13 refs.)
Janus kinases in cytokine signalling (1996)

Hematopoiesis is largely regulated by the binding of cytokines to receptors of the cytokine receptor superfamily. Although lacking catalytic domains, members of the cytokine receptor superfamily mediate ligand dependent activation of tyrosine phosphorylation which is critical for all receptor functions. Recent studies have demonstrated that this is mediated through the association and activation of members of the Janus kinase (Jak) family of protein tyrosine kinases. The activated Jaks phosphorylate the receptors, creating docking sites for SH2 containing signalling proteins which are tyrosine phosphorylated following their association with the receptor complex. Among the substrates of tyrosine phosphorylation are members of the signal transducers and activators of transcription family of proteins (Stats). Various cytokines induce the tyrosine phosphorylation and activation of one or more of the six family members. The pattern of Stat activation provides a level of cytokine individuality that is not observed in the activation of other signalling pathways. Although not required for mitogenic responses, it is speculated that the Stats may mediate many of the cytokine specific functional responses of hematopoietic cells.
Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions (2004)

Gram-negative bacteria have five major subcellular localization sites: the cytoplasm, the periplasm, the inner membrane, the outer membrane, and the extracellular space. The subcellular location of a protein can provide valuable information about its function. With the rapid increase of sequenced genomic data, the need for an automated and accurate tool to predict subcellular localization becomes increasingly important. We present an approach to predict subcellular localization for Gram-negative bacteria. This method uses the support vector machines trained by multiple feature vectors based on n-peptide compositions. For a standard data set comprising 1443 proteins, the overall prediction accuracy reaches 89%, which, to the best of our knowledge, is the highest prediction rate ever reported. Our prediction is 14% higher than that of the recently developed multimodular PSORT-B. Because of its simplicity, this approach can be easily extended to other organisms and should be a useful tool for the high-throughput and large-scale analysis of proteomic and genomic data.
2016 US lymphoid malignancy statistics by World Health Organization subtypes (2016)

Collectively, lymphoid neoplasms are the fourth most common cancer and the sixth leading cause of cancer death in the United States. The authors provide contemporary lymphoid neoplasm statistics by subtype based on the 2008 World Health Organization classifications, including the most current US incidence and survival data. Presented for the first time are estimates of the total numbers of US lymphoid neoplasm cases by subtype as well as a detailed evaluation of incidence and survival statistics. In 2016, 136,960 new lymphoid neoplasms are expected. Overall lymphoma incidence rates have declined in recent years, but trends vary by subtype. Precursor lymphoid neoplasm incidence rates increased from 2001 to 2012, particularly for B-cell neoplasms. Among the mature lymphoid neoplasms, the fastest increase was for plasma cell neoplasms. Rates also increased for mantle cell lymphoma (males), marginal zone lymphoma, hairy cell leukemia, and mycosis fungoides. Like incidence, survival for both mature T-cell lymphomas and mature B-cell lymphomas varied by subtype and by race. Patients with peripheral T-cell lymphomas had among the worst 5-year relative survival (36%-56%, depending on race/sex), while those with mycosis fungoides had among the best survival (79%-92%). For B-cell lymphomas, 5-year survival ranged from 83% to 91% for patients with marginal zone lymphoma and from 78% to 92% for those with hairy cell leukemia; but the rates were as low as 47% to 63% for patients with Burkitt lymphoma and 44% to 48% for those with plasma cell neoplasms. In general, black men had the lowest survival across lymphoid malignancy subtypes. These contemporary incidence and survival statistics are useful for developing management strategies for these cancers and can offer clues regarding their etiology. CA Cancer J Clin 2016;66:443-459. © 2016 American Cancer Society.
A 10nm platform technology for low power and high performance application featuring FINFET devices with multi workfunction gate stack on bulk and SOI (2014)

A 10nm logic platform technology is presented for low power and high performance application with the tightest contacted poly pitch (CPP) of 64nm and metallization pitch of 48nm ever reported in the FinFET technology on both bulk and SOI substrate. A 0.053um<sup>2</sup> SRAM bit-cell is reported with a corresponding Static Noise Margin (SNM) of 140mV at 0.75V. Intensive multi-patterning technology and various self-aligned processes have been developed with 193i lithography to overcome optical patterning limit. Multi-workfunction (WF) gate stack has been enabled to provide Vt tunability without the variability degradation induced by channel dopants.
Rapid Methods for High-Throughput Detection of Sulfoxides (2009)

Enantiopure sulfoxides are prevalent in drugs and are useful chiral auxiliaries in organic synthesis. The biocatalytic enantioselective oxidation of prochiral sulfides is a direct and economical approach for the synthesis of optically pure sulfoxides. The selection of suitable biocatalysts requires rapid and reliable high-throughput screening methods. Here we present four different methods for detecting sulfoxides produced via whole-cell biocatalysis, three of which were exploited for high-throughput screening. Fluorescence detection based on the acid activation of omeprazole was utilized for high-throughput screening of mutant libraries of toluene monooxygenases, but no active variants have been discovered yet. The second method is based on the reduction of sulfoxides to sulfides, with the coupled release and measurement of iodine. The availability of solvent-resistant microtiter plates enabled us to modify the method to a high-throughput format. The third method, selective inhibition of horse liver alcohol dehydrogenase, was used to rapidly screen highly active and/or enantioselective variants at position V106 of toluene ortho-monooxygenase in a saturation mutagenesis library, using methyl-p-tolyl sulfide as the substrate. A success rate of 89% (i.e., 11% false positives) was obtained, and two new mutants were selected. The fourth method is based on the colorimetric detection of adrenochrome, a back-titration procedure which measures the concentration of the periodate-sensitive sulfide. Due to low sensitivity during whole-cell screening, this method was found to be useful only for determining the presence or absence of sulfoxide in the reaction. The methods described in the present work are simple and inexpensive and do not require special equipment.
Bridging the computation gap between programmable processors and hardwired accelerators (2009)

New media and signal processing applications demand ever higher performance while operating within the tight power constraints of mobile devices. A range of hardware implementations is available to deliver computation with varying degrees of area and power efficiency, from general-purpose processors to application-specific integrated circuits (ASICs). The tradeoff of moving towards more efficient customized solutions such as ASICs is the lack of flexibility in terms of hardware reusability and programmability. In this paper, we propose a customized semi-programmable loop accelerator architecture that exploits the efficiency gains available through high levels of customization, while maintaining sufficient flexibility to execute multiple similar loops. A customized instance of the loop accelerator architecture is generated for a particular loop and then the data and control paths are proactively generalized in an efficient manner to increase flexibility. A compiler mapping phase is then able to map other loops onto the same hardware. The efficiency of the programmable accelerator is compared with non-programmable accelerators and with the OpenRISC 1200 general purpose processor. The programmable accelerator is able to achieve up to 34x better power efficiency and 30x better area efficiency than a simple general purpose processor, while trading off as little as 2x power and area efficiency to the non-programmable accelerator.
The use of photodynamic therapy in dermatology: results of a consensus conference. (2006)

Photodynamic therapy (PDT) has significant promise in improving outcomes of patients with a variety of cutaneous conditions. A group of experts met to review the principles, indications, and clinical benefits of PDT with 5-aminolevulinic acid (ALA). They also reviewed PDT with methyl aminolevulinate. The experts established consensus statements for pretreatment, posttreatment, ALA contact time, light sources, and numbers of sessions associated with ALA PDT for actinic keratosis and superficial basal cell carcinoma, photorejuvenation and cosmetic enhancement, acne, sebaceous skin, rosacea, and rhinophyma. They based consensus recommendations on their clinical experience and the medical literature. They also suggested future applications of ALA PDT. Experts concluded that ALA PDT is a safe and effective modality for the treatment of conditions commonly encountered in dermatology. Since downtime is minimal, the technique is suitable for patients of all ages and lifestyles. Appropriate light sources are available in many dermatology offices. The expanding clinical and financial benefits of PDT justify the purchase of an appropriate light source.
Dual fluorescence of diphenylpolyenes (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDual fluorescence of diphenylpolyenesTakao. Itoh and Bryan E. KohlerCite this: J. Phys. Chem. 1987, 91, 7, 1760–1764Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/j100291a017https://doi.org/10.1021/j100291a017research-articleACS PublicationsRequest reuse permissionsArticle Views324Altmetric-Citations93LEARN 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
CRYOGENIC WASHOUT OF SOLID ROCKET PROPELLANTS (1997)

Cryogenic washout (U.S. Patent No. 5025632) is a process using liquid nitrogen (LN2) as a washout medium to remove propellant from within solid rocket motors. The process is environmentally clean and produces dry, size-reduced particles that are well suited for disposal or for reuse in applications such as commercial explosives. A prototype cryogenic washout facility has been constructed for washout of Minuteman II Stage 3 solid rocket motors under a contract with the U.S. Air Force. Design support testing on a bench-scale system has been completed. Workup and subscale safety tests are in progress. The design support testing included laboratory and bench-scale testing on Hazard Class 1.1 and 1.3 propellants. The laboratory tests established that essentially no change in the sensitivity of the test propellants occurred between ambient and cryogenic temperatures. This paper describes prototype equipment design and presents a summary of the testing performed.
Leucine-rich Repeat Kinase 2 (LRRK2) Pharmacological Inhibition Abates α-Synuclein Gene-induced Neurodegeneration (2015)

Therapeutic approaches to slow or block the progression of Parkinson disease (PD) do not exist. Genetic and biochemical studies implicate α-synuclein and leucine-rich repeat kinase 2 (LRRK2) in late-onset PD. LRRK2 kinase activity has been linked to neurodegenerative pathways. However, the therapeutic potential of LRRK2 kinase inhibitors is not clear because significant toxicities have been associated with one class of LRRK2 kinase inhibitors. Furthermore, LRRK2 kinase inhibitors have not been tested previously for efficacy in models of α-synuclein-induced neurodegeneration. To better understand the therapeutic potential of LRRK2 kinase inhibition in PD, we evaluated the tolerability and efficacy of a LRRK2 kinase inhibitor, PF-06447475, in preventing α-synuclein-induced neurodegeneration in rats. Both wild-type rats as well as transgenic G2019S-LRRK2 rats were injected intracranially with adeno-associated viral vectors expressing human α-synuclein in the substantia nigra. Rats were treated with PF-06447475 or a control compound for 4 weeks post-viral transduction. We found that rats expressing G2019S-LRRK2 have exacerbated dopaminergic neurodegeneration and inflammation in response to the overexpression of α-synuclein. Both neurodegeneration and neuroinflammation associated with G2019S-LRRK2 expression were mitigated by LRRK2 kinase inhibition. Furthermore, PF-06447475 provided neuroprotection in wild-type rats. We could not detect adverse pathological indications in the lung, kidney, or liver of rats treated with PF-06447475. These results demonstrate that pharmacological inhibition of LRRK2 is well tolerated for a 4-week period of time in rats and can counteract dopaminergic neurodegeneration caused by acute α-synuclein overexpression.