gebhart/patrepeval huggingface dataset:
T cell recognition of hapten. Anatomy of T cell receptor binding of a H-2Kd-associated photoreactive peptide derivative. (1999)

Page 3629, Table I: Table I is missing a line between contact 11 and 12. Also, contact 23 is a hydrogen bond and should have an asterisk in the “Distance” column. The correct table is printed below.Table IT1 TCR-ligand contacts predicted by modelContact No.LocationTCRLigandDistanceaAsterisks denote hydrogen bonds; no asterisk signifies van der Waals or polar contacts.InhibitionbInhibition of T1 TCR photoaffinity labeling upon mutation.TCRLigandÅ%1CDR1αThr26OG1cAs observed for A6 TCR (21).KdGlu58OE13.0*2CDR1αThr27OG1dAs observed for 2C TCR (23).KdGlu58OE13.2*993CDR1αTyr29OHdAs observed for 2C TCR (23).KdGlu62OE12.6*994CDR2αLys48NZdAs observed for 2C TCR (23).KdGlu154OE12.8*585CDR2αLys48NZKdTyr155OH2.9*926CDR2αThr51OG1cAs observed for A6 TCR (21).,dAs observed for 2C TCR (23).KdAla158CB3.3787CDR2αAsn53ND2cAs observed for A6 TCR (21).KdGlu166OE23.5*58608CDR3αArg94OPbCS Pro255CG3.1909CDR3αGly95CAPbCS Pro255CB3.210CDR3αAsn96ND2ABAeNonstandard atom designation used for ABA.OF2.8*9611CDR3αAsn96NPbCS Pro255O3.3*9611′CDR3αAsn96OD1PbCS Ser256OG3.0*969512CDR3αAsn97CAABACE23.113CDR3αArg99NH1ABAN33.2*8810014CDR3αArg99NH2ABAN33.4*15βN terminusGlu1OE2KdGln149NE22.9*5016CDR1βAsn31OD1ABACE12.7*9917CDR1βAsn31OD1ABACD13.1*9918CDR2βTyr48OHABAN23.65110019CDR2βTyr50OHABACE23.2*6020CDR2βTyr50OHKdGln72OE12.9*606621CDR3βGlu95OE1ABANZ3.1*22CDR3βGln97NE2PbCS Glu258OE13.1*989923CDR3βGln97NPbCS Glu258OE13.0*989924CDR3βGln97NE2KdAsp152OD12.7*9810025CDR3βGln97OE1KdAsp152N2.9*9810026CDR3βSer98OGKdTyr155OH2.9*969227CDR3βTyr99OHKdTyr159OH2.7*a Asterisks denote hydrogen bonds; no asterisk signifies van der Waals or polar contacts.b Inhibition of T1 TCR photoaffinity labeling upon mutation.c As observed for A6 TCR (21).d As observed for 2C TCR (23).e Nonstandard atom designation used for ABA. Open table in a new tab
Future role of gastroenterologists in digestive oncology in the Asia Pacific region: Panir Chelvam Memorial Lecture, Asian Pacific Digestive Week 2010 (2010)

There is an increasing burden in digestive cancer in the coming years. With the advancement of endoscopic therapy, new molecular target therapy and minimally invasive ablation therapy, the treatment of digestive cancer will become more complicated. In Asia where gastric cancer and hepatocellular carcinoma are still prevalent and colorectal cancer is rapidly on the rise, the need in digestive oncology will be even higher. A new subspecialty of digestive oncology will be needed from the patient's perspective, from the healthcare authority's viewpoint and for the future development of gastroenterology.
Determination of Cross Sections by Overtone Mobility Spectrometry: Evidence for Loss of Unstable Structures at Higher Overtones (2010)

Overtone mobility spectrometry (OMS) is examined as a means of determining the collision cross sections for multiply charged ubiquitin and substance P ions, as well as for singly charged rafinose and melezitose ions. Overall, values of collision cross section measured by OMS for stable ion conformations are found to be in agreement with values determined by conventional ion mobility spectrometry (IMS) measurements to within ∼1% relative uncertainty. The OMS spectra for ubiquitin ions appear to favor different conformations at higher overtones. We propose that the changes in the distributions as a function of the overtone region in which they are measured arise from the elimination of ions that undergo structural transitions in the drift regions. Kinetics simulations suggest that structural transitions occurring on the order of a few ms and resulting in an ∼4% change in ion collision cross sections are detected by OMS measurements. The unique method of distinguishing ion mobilities with OMS reveals these structural transitions which are not readily apparent from traditional IMS measurements.
An FPGA with power-gated switch blocks (2012)

Static power consumption is an important component of the total power consumption in FPGAs built using 90nm and smaller technology nodes. A previous study proposed powering down regions of logic blocks in an FPGA when idle to reduce the static power dissipation. This previous work did not consider powering down the switch blocks (SBs). However, the static power of SBs constitute more than 50% of an FPGA's static power. In this paper, we present an architecture that enables selectively powering down SBs along with the logic blocks during their idle periods. The potential power savings from this architecture depends on the proportion of SBs that can be powered down. We present modifications to our CAD flow to maximize the number of such SBs, and we experimentally estimate their proportion using a set of synthetic benchmark circuits. Our estimation results show that 53% to 83% of the SBs can be powered down in a functional module of size 24×24 tiles and an architecture power gating regions of size 4×4 tiles, leading to overall static power reductions of 70% to 84% compared to an architecture that does not support power gating.
Optical improvements of a Z-shaped cell for high-sensitivity UV absorbance detection in capillary electrophoresis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptical improvements of a Z-shaped cell for high-sensitivity UV absorbance detection in capillary electrophoresisStephen E. Moring, Richard T. Reel, and Remco E. J. van SoestCite this: Anal. Chem. 1993, 65, 23, 3454–3459Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/ac00071a020https://doi.org/10.1021/ac00071a020research-articleACS PublicationsRequest reuse permissionsArticle Views483Altmetric-Citations104LEARN 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
Power-law stochastic neighbor embedding (2017)

Stochastic neighbor embedding (SNE) aims to transform the observations in high-dimensional space into a low-dimensional space which preserves neighbor identities by minimizing the Kullback-Leibler divergence of the pairwise distributions between two spaces where Gaussian distributions are assumed. Data visualization could be improved by adopting the t-SNE where Student t distribution is used in the low-dimensional space. However, data pairs in the latent space are forced to be squeezed due to the loss of dimensions. This study incorporates the power-law distribution into construction of the p-SNE. Such an unsupervised p-SNE increases the physical forces in neighbor embedding so that the neighbors in the low-dimensional space can be adjusted flexibly to reflect the neighboring in the high-dimensional space. The experiments on three learning tasks illustrate that the manifold or data structure using the proposed p-SNE is preserved in better shape than that using SNE and t-SNE.
Annealing of Electron-Irradiated n-Type Silicon: Illumination and Fluence Dependence (1971)

The effects of strong illumination and radiation fluence on the annealing behavior of the E center in electron-irradiated phosphorus-doped float-zoned silicon were studied by Hall-effect measurement. Illumination of the sample during anneal increased the rate of recovery significantly. Increasing the radiation fluence and, hence, the level of the induced-carrier compensation, also increased the rate of anneal. These results were found to be consistent with a previously proposed model in which the charge state of the defect was found to be a major determinant of the activation energy of recovery.
Integrated analysis of seed proteome and mRNA oxidation reveals distinct post‐transcriptional features regulating dormancy in wheat (Triticum aestivum L.) (2013)

Wheat seeds can be released from a dormant state by after-ripening; however, the underlying molecular mechanisms are still mostly unknown. We previously identified transcriptional programmes involved in the regulation of after-ripening-mediated seed dormancy decay in wheat (Triticum aestivum L.). Here, we show that seed dormancy maintenance and its release by dry after-ripening in wheat is associated with oxidative modification of distinct seed-stored mRNAs that mainly correspond to oxidative phosphorylation, ribosome biogenesis, nutrient reservoir and α-amylase inhibitor activities, suggesting the significance of post-transcriptional repression of these biological processes in regulating seed dormancy. We further show that after-ripening induced seed dormancy release in wheat is mediated by differential expression of specific proteins in both dry and hydrated states, including those involved in proteolysis, cellular signalling, translation and energy metabolism. Among the genes corresponding to these proteins, the expression of those encoding α-amylase/trypsin inhibitor and starch synthase appears to be regulated by mRNA oxidation. Co-expression analysis of the probesets differentially expressed and oxidized during dry after-ripening along with those corresponding to proteins differentially regulated between dormant and after-ripened seeds produced three co-expressed gene clusters containing more candidate genes potentially involved in the regulation of seed dormancy in wheat. Two of the three clusters are enriched with elements that are either abscisic acid (ABA) responsive or recognized by ABA-regulated transcription factors, indicating the association between wheat seed dormancy and ABA sensitivity.
Factors Affecting Regioselectivity in the Intramolecular Diyl Trapping Reaction (1992)

An account is presented detailing the nature of the factors which allow use of the intramolecular diyl trapping reaction for the selective construction of either linearly fused or bridged cycloadducts. A plan outlining the possible application of the results to the synthesis of the linearly fused tricyclopentanoid Δ9.12-capnellene (1) and of aphidicolin (38), a tetracyclic anticancer agent possessing the bridged substructure, is also presented. 1. Introduction 2. First Evidence for Formation of the Bridged Ring System 3. Original Ideas Concerning Why the Bridged Cycloaddition Product was Obtained 4. Initial Attempts to Selectively Synthesize the Bridged System 4.1. A Frontier Molecular Orbital Argument 4.2. Return to a Reconsideration of the Importance of Geminal Alkyl Substitution 4.3. A Change of Plans - New Focus Upon the Diylophile Substituent 4.4. Intervention of Diyl Spin State Considerations and their Importance with Respect to Regioselectivity 4.5. Similarity Between Monoradical and Triplet Diyl Modes of Closure onto an Alkene 4.6. ESR Evidence for Intervention of the Triplet 4.7. Time to Think Again. How can Bridged Cycloadducts be Obtained Selectively? 4.8. Success at Last. Useful Generalizations Concerning How to Achieve Selectivity 4.9. Rationale 4.10. Application to Aphidicolin? 4.11. "Correction" of our Initial Analysis Error: Δ9.12Capnellene Revisited 5. Concluding Remarks
A Novel Approach to the Synthesis of Precursors of Tricyclic β-Lactam Antibiotics (1999)

The stereoselective synthesis of two precursors of tricyclic β-lactam antibiotics (trinems) has been attempted by a novel approach that involves a highly stereoselective azetidinone ring-forming reaction followed by the reduction of a functionalized aromatic substituent at C-4 of the β-lactam nucleus.
Cache-oblivious algorithms (2003)

This paper presents asymptotically optimal algorithms for rectangular matrix transpose, FFT, and sorting on computers with multiple levels of caching. Unlike previous optimal algorithms, these algorithms are cache oblivious: no variables dependent on hardware parameters, such as cache size and cache-line length, need to be tuned to achieve optimality. Nevertheless, these algorithms use an optimal amount of work and move data optimally among multiple levels of cache. For a cache with size Z and cache-line length L where Z=/spl Omega/(L/sup 2/) the number of cache misses for an m/spl times/n matrix transpose is /spl Theta/(1+mn/L). The number of cache misses for either an n-point FFT or the sorting of n numbers is /spl Theta/(1+(n/L)(1+log/sub Z/n)). We also give an /spl Theta/(mnp)-work algorithm to multiply an m/spl times/n matrix by an n/spl times/p matrix that incurs /spl Theta/(1+(mn+np+mp)/L+mnp/L/spl radic/Z) cache faults. We introduce an "ideal-cache" model to analyze our algorithms. We prove that an optimal cache-oblivious algorithm designed for two levels of memory is also optimal for multiple levels and that the assumption of optimal replacement in the ideal-cache model. Can be simulated efficiently by LRU replacement. We also provide preliminary empirical results on the effectiveness of cache-oblivious algorithms in practice.
Lifetime Risk for Blindness in Eyes with Open-Angle Glaucoma (2012)

One eye per patient was included in the analysis. If both eyes had glaucoma one was randomly selected. We recorded the extent of visual field loss (as Mean Deviation) and visual acuity (VA) at the time of diagnosis and at the last visit. Beside, we calculated the widest diameter of the remaining central visual field (Figure 4). Low vision and blindness were defined according to WHO criteria, and the major reason for either was noted. The risk for blindness from glaucoma was analyzed by cumulative incidence calculation.
Galactose Oxidase from Fusarium oxysporum - Expression in E. coli and P. pastoris and Biochemical Characterization (2014)

A gene coding for galactose 6-oxidase from Fusarium oxysporum G12 was cloned together with its native preprosequence and a C-terminal His-tag, and successfully expressed both in Escherichia coli and Pichia pastoris. The enzyme was subsequently purified and characterized. Among all tested substrates, the highest catalytic efficiency (kcat/Km) was found with 1-methyl-β-D-galactopyranoside (2.2 mM(-1) s(-1)). The Michaelis constant (Km) for D-galactose was determined to be 47 mM. Optimal pH and temperature for the enzyme activity were 7.0 and 40°C, respectively, and the enzyme was thermoinactivated at temperatures above 50°C. GalOx contains a unique metalloradical complex consisting of a copper atom and a tyrosine residue covalently attached to the sulphur of a cysteine. The correct formation of this thioether bond during the heterologous expression in E. coli and P. pastoris could be unequivocally confirmed by MALDI mass spectrometry, which offers a convenient alternative to prove this Tyr-Cys crosslink, which is essential for the catalytic activity of GalOx.
Relationship between Squamous Cell Carcinoma Antigen and the Clinical Severity of Allergic Rhinitis Caused by Dermatophagoides Farinae and Japanese Cedar Pollen (2010)

These results suggest that the serum SCCA level may be a useful biomarker to evaluate the severity of allergic rhinitis caused by D farinae.
The N-Myc Down Regulated Gene1 (NDRG1) Is a Rab4a Effector Involved in Vesicular Recycling of E-Cadherin (2007)

Cell to cell adhesion is mediated by adhesion molecules present on the cell surface. Downregulation of molecules that form the adhesion complex is a characteristic of metastatic cancer cells. Downregulation of the N-myc down regulated gene1 (NDRG1) increases prostate and breast metastasis. The exact function of NDRG1 is not known. Here by using live cell confocal microscopy and in vitro reconstitution, we report that NDRG1 is involved in recycling the adhesion molecule E-cadherin thereby stabilizing it. Evidence is provided that NDRG1 recruits on recycling endosomes in the Trans Golgi network by binding to phosphotidylinositol 4-phosphate and interacts with membrane bound Rab4aGTPase. NDRG1 specifically interacts with constitutively active Rab4aQ67L mutant protein and not with GDP-bound Rab4aS22N mutant proving NDRG1 as a novel Rab4a effector. Transferrin recycling experiments reveals NDRG1 colocalizes with transferrin during the recycling phase. NDRG1 alters the kinetics of transferrin recycling in cells. NDRG1 knockdown cells show a delay in recycling transferrin, conversely NDRG1 overexpressing cells reveal an increase in rate of transferrin recycling. This novel finding of NDRG1 as a recycling protein involved with recycling of E-cadherin will aid in understanding NDRG1 role as a metastasis suppressor protein.
Phrase-level and Word-level Strategies for Detecting Appositions in Speech (2009)

International audience
BX471: A CCR1 Antagonist with Anti-Inflammatory Activity in Man (2005)

Chemokines belong to a large family of chemoattractant molecules involved in the directed migration of immune cells. They achieve their cellular effects by direct interaction with cell surface receptors. The chemokine receptor CCR1 appears to be involved in a variety of proinflammatory and autoimmune diseases and this makes it a very attractive therapeutic target. This review discusses the identification, chemistry, biology and therapeutic potential of BX 471 a potent CCR1 antagonist that is currently in the clinic for a variety of indications.
Placental Protein 13 Administration to Pregnant Rats Lowers Blood Pressure and Augments Fetal Growth and Venous Remodeling (2015)

Reduced first-trimester concentrations of placental protein 13 (PP13) are associated with subsequent development of preeclampsia, a major pregnancy disorder. We previously showed that PP13 has a vasodilatory effect, reduces blood pressure and augments expansive remodeling of the uteroplacental vasculature in pregnant rats. In this study, slow-release osmotic pumps were implanted in gravid rats (on day 8) to provide 1 week of PP13 supplementation. Treatment was associated with a reversible blood pressure reduction that returned to normal on day 15. In addition, PP13 caused venous expansion that is larger in the venous branches closer to the placenta. Then, it increased placental and pup weights. Similar administration of a truncated PP13 variant (DelT221) that is unable to bind carbohydrates (a rare spontaneous mutation associated with a high frequency of severe early preeclampsia among Blacks in South Africa) produced a hypotensive effect similar to the full-length molecule, but without venous remodeling and increased placental and pup weights. These results indicate the importance of PP13 carbohydrate binding for inducing vascular remodeling and improving reproductive outcome. Future studies are needed to determine whether beneficial effects would be evident in animal models of preeclampsia or in women predisposed to the development of preeclampsia.
Empirical factors affecting reconstruction of image-guided near infrared spectroscopy (2011)

Empirical factors in image reconstruction that can have a dramatic effect on final image quantification in image guided optical spectroscopy using MRI are examined. We present a model for image segmentation that finds that tumor region quantification is influenced by defined size of that region, and we conclude that the most effective segmentation is done using a ktrans map to define the tumor region along with guidance from a radiologist experienced in breast MRI. Data calibration also introduces another empirical factor and we weigh advantages and disadvantages of different methods of calibrating data based on imaging geometry and volume. Finally, we investigate the effects of a modified Levenburg- Marquardt reconstruction that uses a regularization parameter to make the reconstruction less ill-posed and limit the effects of image noise. We find that the regularization parameter must fall within a certain range to adequately smooth the image but if it is too large then image contrast is lost. Understanding and minimizing these factors' contribution will be increasingly important as MRI/NIRS becomes closer to clinical use to ensure that the best possible images are always produced to aid in prognostic clinical decisions.
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts (2016)

The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic "birthday" trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.
Assessment of transient myocardial perfusion defects in intact mice using a microbubble contrast destruction / refill approach (2005)

The mouse provides a very useful model for human cardiovascular disease. Consequently, there is significant need for noninvasive approaches for assessing left ventricular function in the setting of various cardiovascular pathophysiological conditions induced in normal and genetically-modified mice. In this work, myocardial contrast echocardiography (MCE) was used to identify regions of ischemia within ultrasound images of the left ventricular myocardium in closed-chest, intact mice. Contrast agent was infused at a constant rate and, periodically, high intensity, contrast destructive frames were applied. Thereafter, an exponential refill curve was fitted to the mean gray scale value within the selected region of interest. Perfusion was investigated before, during and immediately after an induced ischemic event. As anticipated, a significantly reduced refill rate was observed during ischemia. The refill exponential rate constant was observed to decline by 35% in the region of myocardium affected by the induced ischemia.