gebhart/patrepeval huggingface dataset:
EFFECTIVE BIO-EVENT EXTRACTION USING TRIGGER WORDS AND SYNTACTIC DEPENDENCIES (2011)

The scientific literature is the main source for comprehensive, up-to-date biological knowledge. Automatic extraction of this knowledge facilitates core biological tasks, such as database curation and knowledge discovery. We present here a linguistically inspired, rule-based and syntax-driven methodology for biological event extraction. We rely on a dictionary of trigger words to detect and characterize event expressions and syntactic dependency based heuristics to extract their event arguments. We refine and extend our prior work to recognize speculated and negated events. We show that heuristics based on syntactic dependencies, used to identify event arguments, extend naturally to also identify speculation and negation scope. In the BioNLP’09 Shared Task on Event Extraction, our system placed third in the Core Event Extraction Task (F-score of 0.4462), and first in the Speculation and Negation Task (F-score of 0.4252). Of particular interest is the extraction of complex regulatory events, where it scored second place. Our system significantly outperformed other participating systems in detecting speculation and negation. These results demonstrate the utility of a syntax-driven approach. In this article, we also report on our more recent work on supervised learning of event trigger expressions and discuss event annotation issues, based on our corpus analysis.
Silencer! A tool for substrate noise coupling analysis (2004)

Silencer! is a new, fully automated, substrate noise coupling analysis tool that is integrated into the CADENCE DFII design environment. This tool seamlessly enables substrate noise coupling analysis in a standard mixed-signal design flow. IC designers can analyze substrate noise coupling at different levels of hierarchy - from the schematic level to the layout. Examples have been simulated and the results are accurate to within 10% of measured fabricated chips.
Computational Complexity of Test-Point Insertions and Decompositions (2005)

We consider two basic computational problems that arise in the areas of pseudo-exhaustive testing, design, of polynomial-time testable classes, test-point inuertion, and Crosscheck, in the context of test generation and design for testability of combinational circuits. The first problem is to decom.pose a circuit info subcircuits such that the number of inputs to each subcircuit is bounded by I<; we show that this problem is NP-complete. This result establishes that the detection (minimization) problems associated with three polynomial-time testable classes and the method of pseudo-exhaustive testing are all NP-complete (hard). We then present simple approximation algorith.ms for solving these problems. The second problem deals with placing k test points on a circuit so as to facilitate the observability and/or controllability; this problem is also shown to be NP-hard. This problem arises in, the methods of Crosscheck and segment-cell placem.ent. 1 Tnt roduct ion There are several methods in the area of test generation and design for testability, and in these methods some basic computational problems appear in disguises in seemingly different contexts. We consider two such problems: circuit decompositions with bounded number of inputs for each subcircuit, and computing a subset of nets which can be used to inject and/or inspect signals. The first problem arises in the design of polynomial-time testable classes of combinational circuits [2,3,13], and in the method of pseudo-exhaustive testing [6,9,113. The second problem occurs in the method of segment cell placement [15] and in some parts of the method of CrossCIieck [16]. Despite the differences in the origins of their
Amplified Expression, Purification and Functional Reconstitution of the Dipeptide and Tripeptide Transport Protein of <i>Lactococcus Lactis</i> (1997)

Transport of hydrophilic dipeptides and tripeptides into Lactococcus lactis is mediated by a proton-motive-force-driven peptide-transport protein (DtpT) that shares similarity to eukaryotic peptide transporters, e.g. from yeasts, plants, and the kidney and small intestine of rabbit, man and rat. The expression level of DtpT protein in L. lactis was increased (20-40-fold) to approximately 10% of total integral membrane protein by means of a low-copy-number vector and selecting the appropriate growth conditions. Membrane vesicles bearing the DtpT-His6 protein (containing a C-terminal factor-Xa cleavage site and a six-histidine-tag) showed a Pro-Ala uptake activity that was half that of membranes containing the wild-type protein. The activity in the DtpT-His6 membrane vesicles increased at least 50% upon removal of the His6 tag from the protein. More than 95% DtpT was solubilized from L. lactis membranes in the presence of 1% (mass/vol.) n-dodecyl-beta-D-maltoside, and approximately 2 mg DtpT-His6 was purified by Ni2+-chelate affinity chromatography from 100 mg membrane protein. Purified DtpT-His6 was reconstituted unidirectionally into detergent-saturated formed liposomes, which were prepared from Escherichia coli phospholipid and egg phosphatidylcholine; the detergent was removed by adsorption to polystyrene beads. The highest uptake activities were obtained when DtpT was incorporated into liposomes that were treated with a low amount of n-dodecyl-beta-D-maltoside (onset of liposome solubilization). The uptake activity could be improved by addition of NaCl (200 mM) and lipids (2 mg/ml) during the solubilization, purification and reconstitution steps.
Linear quadratic state feedback and robust neural network estimator for field-oriented-controlled induction motors (1999)

A field-oriented control scheme for an induction motor with a linear quadratic optimal regulator and a robust neural network estimator is proposed. The state feedback is designed by using the synchronous frame motor model. The number of the states is increased in order to take into account the presence of two integrators on the flux and torque errors. The resulting model is suitably simplified and the corresponding approximations are discussed. The procedure proposed is shown to be suitable also for the design of the state feedback via the pole placement technique. A comparison with standard proportional integral regulators is provided. The rotor flux is estimated by using a robust neural network observer. The network training set is suitably designed in order to preserve the drive effectiveness also in the presence of large parameter uncertainties. The robust neural observer is compared with an extended Kalman filter and a standard neural network observer. Using a 250 kW induction motor as a case study, the simulation results show the effectiveness of the proposed solution, both during transient and steady-state operating conditions.
A Low-Power Magnitude Detector for Analysis of Transient-Rich Signals (2012)

Magnitude detection, such as envelope detection or RMS estimation, is needed for many low-power signal-analysis applications. In such applications, the temporal accuracy of the magnitude detector is as important as its amplitude accuracy. We present a low-power audio-frequency magnitude detector that simultaneously achieves both high temporal accuracy and high amplitude accuracy. This performance is achieved by rectifying the signal with a high-ripple peak detector and then averaging this rectified signal with an adaptive-time-constant filter. The time constant of this filter decreases with increasing amplitude, enabling the filter to quickly respond on a short time scale to transients, while steady-state ripple is averaged on a longer time scale. The circuit has been fabricated in a 0.18 μm CMOS process and consumes only 1.1 nW-1.08 μW when tuned for operation from 20 Hz-20 kHz. It exhibits a dynamic range of 70 dB across typical speech frequencies.
Molecular Characteristics of RAGE and Advances in Small-Molecule Inhibitors (2021)

Receptor for advanced glycation end-products (RAGE) is a member of the immunoglobulin superfamily. RAGE binds and mediates cellular responses to a range of DAMPs (damage-associated molecular pattern molecules), such as AGEs, HMGB1, and S100/calgranulins, and as an innate immune sensor, can recognize microbial PAMPs (pathogen-associated molecular pattern molecules), including bacterial LPS, bacterial DNA, and viral and parasitic proteins. RAGE and its ligands stimulate the activations of diverse pathways, such as p38MAPK, ERK1/2, Cdc42/Rac, and JNK, and trigger cascades of diverse signaling events that are involved in a wide spectrum of diseases, including diabetes mellitus, inflammatory, vascular and neurodegenerative diseases, atherothrombosis, and cancer. Thus, the targeted inhibition of RAGE or its ligands is considered an important strategy for the treatment of cancer and chronic inflammatory diseases.
Add-on laser reading device for a camera phone (2005)

A novel add-on device to a mobile camera phone has been developed. The prototype system contains both laser and LED illumination as well as imaging optics. Main idea behind the device is to have a small printable diffractive ROM (Read Only Memory) element, which can be read by illuminating it with a laser-beam and recording the resulting datamatrix pattern with a camera phone. The element contains information in the same manner as a traditional bar-code, but due to the 2D-pattern and diffractive nature of the tag, a much larger amount of information can be packed on a smaller area. Optical and mechanical designs of the prototype device have been made in such a way that the system can be used in three different modes: as a laser reader, as a telescope and as a microscope.
Inhibition of <i>Listeria monocytogenes</i> in Fish and Meat Systems by Use of Oregano and Cranberry Phytochemical Synergies (2004)

Optimized phenolics from oregano and cranberry extracts were evaluated for antimicrobial activity against Listeria monocytogenes in laboratory media and in beef and fish. The antimicrobial activity increased when oregano and cranberry extracts were mixed at a ratio of 75% oregano and 25% cranberry (wt/wt) with 0.1 mg of phenolic per disk or ml, and the efficacy was further enhanced by lactic acid. The inhibition by phytochemical and lactic acid synergies was most effective when beef and fish slices were stored at 4 degrees C.
A statistical problem for inference to regulatorystructure from associations of gene expression measurements withmicroarrays (2003)

This paper describes an elementary statistical difficulty for all such procedures, no matter whether based on Bayesian updating, conditional independence testing, or other machine learning procedures such as simulated annealing or neural net pruning. The difficulty obtains if a number of cells from a common population are aggregated in a measurement of expression levels. Although there are special cases where the conditional associations are preserved under aggregation, in general inference of genetic regulatory structure based on conditional association is unwarranted
SecSpace (2014)

Privacy mechanisms are important in mixed-presence (collocated and remote) collaborative systems. These systems try to achieve a sense of co-presence in order to promote fluid collaboration, yet it can be unclear how actions made in one location are manifested in the other. This ambiguity makes it difficult to share sensitive information with confidence, impacting the fluidity of the shared experience. In this paper, we focus on mixed reality approaches (blending physical and virtual spaces) for mixed presence collaboration. We present SecSpace, our software toolkit for usable privacy and security research in mixed reality collaborative environments. SecSpace permits privacy-related actions in either physical or virtual space to generate effects simultaneously in both spaces. These effects will be the same in terms of their impact on privacy but they may be functionally tailored to suit the requirements of each space. We detail the architecture of SecSpace and present three prototypes that illustrate the flexibility and capabilities of our approach.
Interlaminar reinforcement of carbon fiber composites from unidirectional prepreg utilizing aligned carbon nanotubes (2016)

Thesis: S.M., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2016.
The tyrosine kinase inhibitor dasatinib acts as a pharmacologic on/off switch for CAR T cells (2019)

Immunotherapy with chimeric antigen receptor (CAR)-engineered T cells can be effective against advanced malignancies. CAR T cells are "living drugs" that require technologies to enable physicians (and patients) to maintain control over the infused cell product. Here, we demonstrate that the tyrosine kinase inhibitor dasatinib interferes with the lymphocyte-specific protein tyrosine kinase (LCK) and thereby inhibits phosphorylation of CD3ζ and ζ-chain of T cell receptor-associated protein kinase 70 kDa (ZAP70), ablating signaling in CAR constructs containing either CD28_CD3ζ or 4-1BB_CD3ζ activation modules. As a consequence, dasatinib induces a function-off state in CD8<sup>+</sup> and CD4<sup>+</sup> CAR T cells that is of immediate onset and can be sustained for several days without affecting T cell viability. We show that treatment with dasatinib halts cytolytic activity, cytokine production, and proliferation of CAR T cells in vitro and in vivo. The dose of dasatinib can be titrated to achieve partial or complete inhibition of CAR T cell function. Upon discontinuation of dasatinib, the inhibitory effect is rapidly and completely reversed, and CAR T cells resume their antitumor function. The favorable pharmacodynamic attributes of dasatinib can be exploited to steer the activity of CAR T cells in "function-on-off-on" sequences in real time. In a mouse model of cytokine release syndrome (CRS), we demonstrated that a short treatment course of dasatinib, administered early after CAR T cell infusion, protects a proportion of mice from otherwise fatal CRS. Our data introduce dasatinib as a broadly applicable pharmacologic on/off switch for CAR T cells.
The Genetic Evolution of Melanoma from Precursor Lesions (2015)

Our study defined the succession of genetic alterations during melanoma progression, showing distinct evolutionary trajectories for different melanoma subtypes. It identified an intermediate category of melanocytic neoplasia, characterized by the presence of more than one pathogenic genetic alteration and distinctive histopathological features. Finally, our study implicated ultraviolet radiation as a major factor in both the initiation and progression of melanoma. (Funded by the National Institutes of Health and others.).
Tunnel current measurements on P/N junction diodes and implications for future device design (2004)

Band-to-band tunneling was studied experimentally in ion-implanted PN junction diodes with profiles representative of present and future silicon CMOS transistors. Measurements were done over a wide range of temperatures and implant parameters. Profile parameters were derived from analysis of CV characteristics, and compared to SIMS analysis. When tunneling current was plotted against distance (tunneling distance, corrected for band curvature) a quasi-universal exponential reduction of tunneling current vs. tunneling distance was found with an attenuation length of 0.38 nm, and an extrapolated tunneling current at zero tunnel distance of 5.3/spl times/10/sup 7/ A/cm/sup 2/ at 300 K. These results were used to estimate drain-substrate currents in future scaled CMOS, and it was concluded that it will be challenging to make the ITRS 2002 roadmap projections on leakage current for the low operating power and low standby power options without more innovation and device design changes.
Thymic-Specific Serine Protease Limits Central Tolerance and Exacerbates Experimental Autoimmune Encephalomyelitis (2017)

The genetic predisposition to multiple sclerosis (MS) is most strongly conveyed by MHC class II haplotypes, possibly by shaping the autoimmune CD4 T cell repertoire. Whether Ag-processing enzymes contribute to MS susceptibility by editing the peptide repertoire presented by these MHC haplotypes is unclear. Thymus-specific serine protease (TSSP) is expressed by thymic epithelial cells and thymic dendritic cells (DCs) and, in these two stromal compartments, TSSP edits the peptide repertoire presented by class II molecules. We show in this article that TSSP increases experimental autoimmune encephalomyelitis severity by limiting central tolerance to myelin oligodendrocyte glycoprotein. The effect on experimental autoimmune encephalomyelitis severity was MHC class II allele dependent, because the lack of TSSP expression conferred protection in NOD mice but not in C57BL/6 mice. Importantly, although human thymic DCs express TSSP, individuals segregate into two groups having a high or 10-fold lower level of expression. Therefore, the level of TSSP expression by thymic DCs may modify the risk factors for MS conferred by some MHC class II haplotypes.
Genetic and isotope ratio mass spectrometric evidence for the occurrence of starch degradation and cycling in illuminated Arabidopsis leaves (2017)

Although there is a great wealth of data supporting the occurrence of simultaneous synthesis and breakdown of storage carbohydrate in many organisms, previous 13CO2 pulse-chase based studies indicated that starch degradation does not operate in illuminated Arabidopsis leaves. Here we show that leaves of gwd, sex4, bam4, bam1/bam3 and amy3/isa3/lda starch breakdown mutants accumulate higher levels of starch than wild type (WT) leaves when cultured under continuous light (CL) conditions. We also show that leaves of CL grown dpe1 plants impaired in the plastidic disproportionating enzyme accumulate higher levels of maltotriose than WT leaves, the overall data providing evidence for the occurrence of extensive starch degradation in illuminated leaves. Moreover, we show that leaves of CL grown mex1/pglct plants impaired in the chloroplastic maltose and glucose transporters display a severe dwarf phenotype and accumulate high levels of maltose, strongly indicating that the MEX1 and pGlcT transporters are involved in the export of starch breakdown products to the cytosol to support growth during illumination. To investigate whether starch breakdown products can be recycled back to starch during illumination through a mechanism involving ADP-glucose pyrophosphorylase (AGP) we conducted kinetic analyses of the stable isotope carbon composition (δ13C) in starch of leaves of 13CO2 pulsed-chased WT and AGP lacking aps1 plants. Notably, the rate of increase of δ13C in starch of aps1 leaves during the pulse was exceedingly higher than that of WT leaves. Furthermore, δ13C decline in starch of aps1 leaves during the chase was much faster than that of WT leaves, which provides strong evidence for the occurrence of AGP-mediated cycling of starch breakdown products in illuminated Arabidopsis leaves.
Temporal Control of Efficient <i>In Vivo</i> Bioconjugation Using a Genetically Encoded Tetrazine-Mediated Inverse-Electron-Demand Diels–Alder Reaction (2020)

An inverse-electron-demand Diels-Alder (IEDDA) reaction using genetically encoded tetrazine variants enables rapid bioconjugation for diverse applications <i>in vitro</i> and <i>in cellulo</i>. However, <i>in vivo</i> bioconjugation using genetically encoded tetrazine variants is challenging, because the IEDDA coupling reaction competes with rapid elimination of reaction partners <i>in vivo</i>. Here, we tested the hypothesis that a genetically encoded phenylalanine analogue containing a hydrogen-substituted tetrazine (frTet) would increase the IEDDA reaction rate, thereby allowing for successful bioconjugation <i>in vivo</i>. We found that the <i>in vitro</i> IEDDA reaction rate of superfolder green fluorescent protein (sfGFP) containing frTet (sfGFP-frTet) was 12-fold greater than that of sfGFP containing methyl-substituted tetrazine (sfGFP-Tet_v2.0). Additionally, sfGFP variants encapsulated with chitosan-modified, pluronic-based nanocarriers were delivered into nude mice or tumor-bearing mice for <i>in vivo</i> imaging. The <i>in vivo</i>-delivered sfGFP-frTet exhibited almost complete fluorescence recovery upon addition of trans-cyclooctene via the IEDDA reaction within 2 h, whereas sfGFP-Tet_v2.0 did not show substantial fluorescence recovery. These results demonstrated that the genetically encoded frTet allows an almost complete IEDDA reaction <i>in vivo</i> upon addition of trans-cyclooctene, enabling temporal control of <i>in vivo</i> bioconjugation in a very high yield.
Determination of the nitrogen chemical structures in petroleum asphaltenes using XANES spectroscopy (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the nitrogen chemical structures in petroleum asphaltenes using XANES spectroscopySudipa Mitra-Kirtley, Oliver C. Mullins, Jan Van Elp, Simon J. George, Jie Chen, and Stephen P. CramerCite this: J. Am. Chem. Soc. 1993, 115, 1, 252–258Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/ja00054a036https://doi.org/10.1021/ja00054a036research-articleACS PublicationsRequest reuse permissionsArticle Views951Altmetric-Citations194LEARN 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
Psychosocial Outcomes of Young Adults Born Very Low Birth Weight (2013)

Despite some evidence of health, educational, and social difficulties, former VLBW young adults obtained similar scores across many aspects of health and social functioning as their same age peers, with some differences largely confined to those with previous disability.
在改进与创新中求发展——伺服驱动装置需要“挟带”针对性技术服务一同销售 (2008)

现场总线系统典型的应用领域是管道控制部件的自动化。一方面，为了保证管道控制阀的正常功能，从而保证可靠的管道输送；另一方面也为了避免灾难性的停产事故，流程工业企业的控制中心要随时能够操控元器件（开启和关闭）。因此，在流程设备控制系统与管道元器件的伺服驱动装置之间必须有很高的通信可靠性。
ATM shared-memory switching architectures (1994)

ATM will provide flexibility in bandwidth allocation and will allow a network to carry heterogeneous services ranging from narrowband to wideband services. The challenge is to build fast packet switches able to match the high speeds of the input links and the high performance requirements imposed. The CCITT has standardized the asynchronous transfer mode (ATM) as the multiplexing and switching principle for the broadband integrated services digital network (B-ISDN). ATM is a packet and connection-oriented transfer mode based on statistical time division multiplexing techniques. The information flow is organized in fixed-size packets called cells, consisting of a user information field (48 octets) and a header (5 octets). The primary use of the header tag is to identify cells belonging to the same virtual channel and to make routing possible. Cell sequence on a virtual channel is preserved, a very low cell loss probability must be guaranteed (< 10/sup -/12), and intensive error and flow control protocols are provided at the edges of the network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>