gebhart/patrepeval huggingface dataset:
Growth‐dependent variation of major histocompatibility complex (MHC) restriction and expression of Ly‐2 and CD3/α/βT cell receptor in cloned cytotoxic T cells (1988)

The specificity of major histocompatibility complex (MHC)-restricted antigen recognition by cytotoxic T cells (CTL) has been clearly correlated to the alpha/beta T cell receptor (TcR) complex on the T cell surface. Occasional changes in the specificity of in vitro cultivated CTL clones, therefore, have been suspected to result from alterations of the genes coding for the TcR alpha and/or beta chain. Here we demonstrate that pronounced variations in the stringency of MHC restriction, previously reported to occur during long-term culture of 2,4,6-trinitrophenyl (TNP)-specific CTL clones, may occur rapidly in a growth-dependent, reversible manner, i.e. without structural TcR variation. Several H-2b TNP-specific CTL clones were shown to possess strong cross-reactivity for H-2k TNP target cells when seeded at low cell numbers, but exhibit reduced or undetectable cross-reaction to H-2k TNP in high-density cultures. Another clone revealed "heteroclitic" properties with significantly stronger cytotoxic activity towards allogeneic (H-2k) than syngeneic (H-2b) TNP-modified target cells. In this case dilute cultures appeared as exclusively allo-MHC restricted, whereas dense cultures were allo/self cross-restricted. In all instances these phenomena were accompanied by cell density-dependent quantitative changes in the expression of Ly-2 and T cell antigen receptor. CTL from dilute cultures had at least 2-fold higher surface concentrations of Ly-2 and CD3 antigens than cells from dense cultures while other surface markers such as Thy-1 or LFA-1 were completely identical. No such effects were observed for CTL clones exhibiting cell density-independent specificity patterns. We conclude from these findings that (a) the stringency of MHC restriction specificity may be significantly affected by the amount of expressed TcR and/or Ly-2 molecules, (b) CTL possess mechanisms to regulate Ly-2 and TcR expression and, hence, their MHC-restricted antigen recognition, and (c) the ability to regulate Ly-2 and TcR expression may be altered during prolonged culture of a CTL clone.
Correction to Selective Class I Phosphoinositide 3-Kinase Inhibitors: Optimization of a Series of Pyridyltriazines Leading to the Identification of a Clinical Candidate, AMG 511 (2012)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Selective Class I Phosphoinositide 3-Kinase Inhibitors: Optimization of a Series of Pyridyltriazines Leading to the Identification of a Clinical Candidate, AMG 511Mark H. Norman*, Kristin L. Andrews, Yunxin Y. Bo, Shon K. Booker, Sean Caenepeel, Victor J. Cee, Noel D. D'Angelo, Daniel J. Freeman, Bradley J. Herberich, Fang-Tsao Hong, Claire L. M. Jackson, Jian Jiang, Brian A. Lanman, Longbin Liu, John D. McCarter, Erin L. Mullady, Nobuko Nishimura, Liping H. Pettus, Anthony B. Reed, Tisha San Miguel, Adrian L. Smith, Markian M. Stec, Seifu Tadesse, Andrew Tasker, Divesh Aidasani, Xiaochun Zhu, Raju Subramanian, Nuria A. Tamayo, Ling Wang, Douglas A. Whittington, Bin Wu, Tian Wu, Ryan P. Wurz, Kevin Yang, Leeanne Zalameda, Nancy Zhang, and Paul E. HughesCite this: J. Med. Chem. 2012, 55, 20, 8975Publication Date (Web):October 12, 2012Publication History Published online12 October 2012Published inissue 25 October 2012https://pubs.acs.org/doi/10.1021/jm301439jhttps://doi.org/10.1021/jm301439jcorrectionACS PublicationsCopyright © 2012 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views696Altmetric-Citations2LEARN 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 PDF (112 KB) Get e-Alertsclose Get e-Alerts
Pancreas preservation for pancreas and islet transplantation (2008)

Cold storage may be adequate for preservation before pancreas transplants, but insufficient when pancreases are processed for islets or when expanded donors are used. Supplementation of cold storage solutions with cytoprotective agents and perfusion may improve pancreas and islet transplant outcomes.
Comparative Analysis of the Olfactory Properties of Silicon/Germanium/Tin Analogues of the Lily‐of‐the‐Valley Odorants Lilial and Bourgeonal (2014)

Abstract The silicon/germanium/tin analogues of the lily‐of‐the‐valley odorants lilial ( rac ‐ 1 a ), compounds rac ‐ 1 b , rac ‐ 1 c , and rac ‐ 1 d , and bourgeonal ( 2 a ), compounds 2 b , 2 c , and 2 d , were synthesized and characterized for their olfactory properties, including GC–olfactometry studies. Compounds rac ‐ 1 a – c and 2 a – c possess a typical lily‐of‐the‐valley odor, whereas the stanna‐analogues rac ‐ 1 d and 2 d , despite some floral aspects, clearly no longer belong to the lily‐of‐the‐valley family. In both series of the carbon/silicon/germanium/tin analogues studied, the lily‐of‐the‐valley odor decreases in the order of carbon&lt;silicon&lt;germanium&lt;tin. A HEK293 cell line with stable tetracycline‐regulated expression of hOR17‐4 was generated to analyze recombinant hOR17‐4 activation by rac ‐ 1 a – d and 2 a – d by using Ca 2+ imaging. Bourgeonal ( 2 a ) showed the highest activation potency, whereas lilial ( rac ‐ 1 a ) and sila‐bourgeonal ( 2 b ) exhibited lower activation potencies. Sila‐lilial ( rac ‐ 1 b ), germa‐lilial ( rac ‐ 1 c ), and stanna‐lilial ( rac ‐ 1 d ), as well as germa‐bourgeonal ( 2 c ) and stanna‐bourgeonal ( 2 d ), did not activate heterologously expressed hOR17‐4 at the concentrations tested. The carbon/silicon/germanium/tin switch strategy thus showed that the stanna‐derivatives clearly exceeded the molecular dimensions of the odorant receptor(s) responsible for the recognition of lily‐of‐the‐valley odorants, although the receptor affinity was already affected with the sila‐ and germa‐analogues. These data could later be used in the qualitative and quantitative evaluation of computational receptor models.
The small molecule axl inhibitor BGB324 shows activity against T315I-mutated and BCR-ABL1 wt chronic myeloid leukemia (2014)

Erdmann, R.; Jorgensen, H.; Ben-Batalla, I.; Kruse, N.; Micklem, D.; von Amsberg, G.; Schafhausen, P.; Schultze, A.; Wroblewski, M.; Binder, M.; Cubas-Cordova, M.; Hadlich, T.; Janing, M.; Sawall, S.; Witzke, V.; Lorens, J.; Allan, E.; Mukherjee, L.; Morrison, H.; Cassells, J.; Kröger, N.; Lorens, J. B.; Clark, R.; Koschmieder, Steffen; Vandenberghe, P.; Brümmendorf, Tim Henrik; Hochhaus, A.; Carmeliet, P.; Holyoake, T.; Pantel, K.; Bokemeyer, C.; Loges, S.
Crustal and Thermal Heterogeneities Across the Fram Strait and the Svalbard Margin (2022)

Abstract The lithospheric structure of the Fram Strait and the extent from the Knipovich Ridge to the Barents Sea shelf and Svalbard are poorly understood. Several multi‐geophysical investigations from various campaigns since the 90s along the Western Barents Sea margin and the Northeast Greenland margin resulted in insufficient and contradicting interpretations of the crustal and upper mantle settings in the oceanic and continental domains. New airborne magnetic data across the Knipovich Ridge and west of Svalbard provide new insights, reveal the complexity of the seafloor spreading history of the Arctic Atlantic Ocean, and indicate a European‐Eurasian continent‐ocean boundary located ∼150 km farther west than previously suggested. This new location of the continent‐ocean boundary prompted to revise the existing 2‐D seismic interpretations in terms of crustal domains and tectono‐stratigraphic setting. This is tested using joint 2‐D gravity and magnetic field modeling to derive an improved crust‐mantle model of the study. One recently acquired combined 2‐D controlled source electromagnetic/magneto‐telluric (CSEM/MT) profile across the Mohns Ridge was also modeled with potential field data and provided new insights into the tectonic settings of the crust and the mantle thermal anomalies. This study proposes to unify the various seismic and CSEM/MT interpretations using the new aeromagnetic compilation.
Progress of Chalcogenide Glass Fibers (2007)

High nonlinearity and large IR transparency make these fibers well suited for compact Raman amplifiers, supercontinuum generation and other mid-IR sources. As <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> fiber has record high theoretical gain compared with silica fiber for slow-light applications.
Biomarker Discovery from Uveal Melanoma Secretomes:  Identification of gp100 and Cathepsin D in Patient Serum (2007)

There is a necessity to better characterize uveal melanoma (UM) tumors according to their metastasis potential at an early stage. In this study we report the identification of potential biomarkers by a combination of proteomics-related approaches: the characterization of UM cell secretomes, the analysis of UM autoantibodies, and the differential depleted serum proteome analysis. We describe a possible role of cathepsin D, syntenin, and gp100 in UM as potential biomarkers.
Speech and Spoken Document (2010)

rogress in both speech and language processing has spurred efforts to sup-port applications that rely on spoken—rather than written—language input.A key challenge in moving from text-based documents to such “spoken doc-uments” is that spoken language lacks explicit punctuation and formatting,which can be crucial for good performance. This article describes differentlevels of speech segmentation, approaches to automatically recovering segment bound-ary locations, and experimental results demonstrating impact on several language pro-cessing tasks. The results also show a need for optimizing segmentation for the endtask rather than independently.
ChemInform Abstract: The First Diels‐Alder Adduct of (60)Fullerene with a Tetrathiafulvalene (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Impact of Multi-flow Transponder on Equipment Requirements in IP over Elastic Optical Networks (2013)

We evaluate the elastic optical network performance from the network to node equipment level using a multi-layer network design scheme. Results show that the multi-flow transponder-based network model reduces equipment requirements such as router IFs and transponders compared to mixed-line-rate and bandwidth-variable models.
The effect of high sodium intake and angiotensin antagonist in rabbits with severe and moderate hypertension induced by constriction of one renal artery. (1977)

&lt;p&gt;Boosting is an iterative ensemble-learning paradigm. Every iteration, a weak predictor learns a classification task, taking into account performance achieved in previous iterations. This is done by assigning weights to individual records of the dataset, which are increased if the record is misclassified by the previous weak predictor. Hence, subsequent predictors learn to focus on problematic records in the dataset. Boosting ensembles such as AdaBoost have shown to be effective models at fighting both high variance and high bias, even in challenging situations such as class imbalance. However, some aspects of AdaBoost might imply limitations for its deployment in the real world. On the one hand, focusing on problematic records can lead to overfitting in the presence of random noise. On the other hand, learning a boosting ensemble that assigns higher weights to hard-to-classify people might throw up serious questions in the age of responsible and transparent data analytics; if a bank must tell a customer that they are denied a loan, because the underlying algorithm made a decision specifically focusing the customer since they are hard to classify, this could be legally dubious. To kill these two birds with one stone, we introduce BoostEMM: a variant of AdaBoost where in every iteration of the procedure, rather than boosting problematic records, we boost problematic subgroups as found through Exceptional Model Mining. Boosted records being part of a coherent group should prevent overfitting, and explicit definitions of the subgroups of people being boosted enhances the transparency of the algorithm.&lt;/p&gt;
Web Service Semantics - WSDL-S (2005)

Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article (e.g., payment of royalties). Copies may be requested from IBM T. J. Watson Research Center, P.
New Sequential Carbon-Carbon Bond Forming Reactions. A Samarium(II) Iodide Mediated Vinylogous Barbier Reaction Followed by an Aldol Reaction (1991)

Reduction of 4-(3-iodopropyl)cyclopent-2-en-1-ones 1 and 7 with 2.5 equivalents of samarium(II) iodide in tetrahydrofuran containing 10 equivalents of 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU) produces bicyclic samarium enolates that can be protonated to give simple bicyclo[3.3.0]octan-3-ones, or reacted with aldehydes to give functionalized bicyclo[3.3.0]octan-3-ones. Depending on the structure of the aldehyde, a rapid intramolecular Tishchenko reaction may follow the aldol reaction.
Why is the subendocardium more vulnerable to ischemia? A new paradigm (2010)

Myocardial ischemia is transmurally heterogeneous where the subendocardium is at higher risk. Stenosis induces reduced perfusion pressure, blood flow redistribution away from the subendocardium, and consequent subendocardial vulnerability. We propose that the flow redistribution stems from the higher compliance of the subendocardial vasculature. This new paradigm was tested using network flow simulation based on measured coronary anatomy, vessel flow and mechanics, and myocardium-vessel interactions. Flow redistribution was quantified by the relative change in the subendocardial-to-subepicardial perfusion ratio under a 60-mmHg perfusion pressure reduction. Myocardial contraction was found to induce the following: 1) more compressive loading and subsequent lower transvascular pressure in deeper vessels, 2) consequent higher compliance of the subendocardial vasculature, and 3) substantial flow redistribution, i.e., a 20% drop in the subendocardial-to-subepicardial flow ratio under the prescribed reduction in perfusion pressure. This flow redistribution was found to occur primarily because the vessel compliance is nonlinear (pressure dependent). The observed thinner subendocardial vessel walls were predicted to induce a higher compliance of the subendocardial vasculature and greater flow redistribution. Subendocardial perfusion was predicted to improve with a reduction of either heart rate or left ventricular pressure under low perfusion pressure. In conclusion, subendocardial vulnerability to a acute reduction in perfusion pressure stems primarily from differences in vascular compliance induced by transmural differences in both extravascular loading and vessel wall thickness. Subendocardial ischemia can be improved by a reduction of heart rate and left ventricular pressure.
BCIRG 001 molecular analysis: Identification of prognostic factors in patients (pts) receiving adjuvant therapy for node- positive (N+) breast cancer (BC) (2007)

525 Background: BCIRG 001 (1,491 pts) demonstrated significant superiority of docetaxel/doxorubicin/cyclophosphamide (TAC) over fluorouracil/doxorubicin/cyclophosphamide (FAC) given as adjuvant therapy for N+ operable BC in terms of disease-free survival (DFS) and overall survival (OS) (Martin et al, N Eng J Med, 2005). This ancillary study was aimed to identify tumor-associated factors related to DFS and OS. Methods: Formalin-fixed primary tumors from pts in BCIRG 001 were analysed by immunohistochemistry. Protocol- specified assessment of histological grade (GR), tumor size (TS), estrogen (ER) and progesterone receptors (PR), lymph node status (LN), HER2, MUC1, Mib, p53, Bcl-2, Bax, Bcl-X, Bag-1, tubulin β isotypes II, III and IV, tau protein and detyrosinated a tubulin was performed. Parameters were scored as the percentage of positive cells and analysed as lower or greater than median values. The samples were randomly split into training (2/3) and validation (1/3) sets. Associations between selected parameters and DFS or OS were tested through univariate analyses using the Kaplan Meier method (log-rank test) on the training set. A backward stepwise Cox regression analysis was performed to identify the final model of prognostic factors on the training set. Multivariate analyses were applied to the validation set. Results: 1,350 samples were split into a training (n=906) and a validation (n=444) set. In univariate GR, TS, LN, ER and PR, Mib, tau protein and HER2 were correlated with DFS in both sets. In multivariate ER, PR, TS, LN, Mib (all p&lt;0.01) and tau (p=0.043) were significantly associated with DFS in the training set. In univariate GR, TS, LN, ER and PR, Mib, MUC1, Bcl-2, tubulin III and IV and tau were correlated with OS in both sets, with a trend for p53. In multivariate ER, TS, LN, Mib, p53 (all p&lt;0.01) and PR (p=0.028) were independently correlated with OS in the training set. Conclusions: These data suggest that tau and p53 are independent markers of DFS and OS, respectively, while Mib is correlated with both DFS and OS in pts receiving these forms of adjuvant chemotherapy for N+ BC. Complementary analyses will be presented. No significant financial relationships to disclose.
Supplementary Figure 7 from Tumor-Specific CD8<sup>+</sup> T Cells Expressing Interleukin-12 Eradicate Established Cancers in Lymphodepleted Hosts (2023)

Supplementary Figure 7 from Tumor-Specific CD8&lt;sup&gt;+&lt;/sup&gt; T Cells Expressing Interleukin-12 Eradicate Established Cancers in Lymphodepleted Hosts
Structural Basis for Reaction Mechanism and Drug Delivery System of Chromoprotein Antitumor Antibiotic C-1027 (2000)

Antitumor antibiotic C-1027, which is regarded as a natural model of a drug delivery system, consists of a carrier apoprotein (Apo) and an enediyne chromophore (Chr). We have compared three solution structures of the DNA−Chr complex, Apo−Chr complex, and free Chr determined by high-resolution NMR experiments. The guest molecule, C-1027 chromophore, showed two distinct binding modes fitted to binding sites of the hosts (target DNA and carrier Apo). The novel Chr interacts with DNA through its benzoxazolinate and aminosugar moieties, and also with Apo through the benzoxazolinate and macrocyclic moieties. The superposition of Chrs in these three states clearly revealed conformational deviation of the 16-membered macrocyclic moiety containing an intra-chlorophenol ring. Ab initio calculations supported good correlation between the reactivity and the conformational alteration of Chr induced in the hosts. The present results provide a molecular basis and implication for the host-recognition mode, the reaction mechanism, and the drug delivery system of chromoprotein C-1027.
The Value of Citizen Science to Promote Transit Accessibility (2018)

We propose that citizen science methods can engage riders with disabilities and others in improving public transportation accessibility by documenting and assessing problems and good solutions throughout the system. This will empower riders, resulting in a greater understanding of the transportation system, and improve the feedback loop between rider and provider.
Rohrbreiautomaten für die Ferkelaufzucht - Ein Vergleich zweier Automaten hinsichtlich der biologischen Leistungen und des Verhaltens der Ferkel (2015)

Zwei Rohrbreiautomaten wurden verglichen. LeanMachine hat einen runden Trog. Das Ausdosieren des Futters erfolgt durch die Bewegung horizontal angeordneter Bügel über dem Trog. PigNic hat einen rechteckigen, dreischaligen Trog mit einem mittig angeordneten Dosierkranz. Das Futter war hier deutlich trockener als bei der Vergleichsvariante. Ferkel an LeanMachine Automaten wendeten mehr Fressvorgänge auf als beim Vergleichssystem, um denselben Körpermassezuwachs zu erzielen. Hinsichtlich Aggressionsverhalten und gegenseitigem Besaugen gab es keine signifikanten Differenzen.
A monolithically integrated optical heterodyne receiver (2005)

We demonstrated a monolithically integrated heterodyne receiver consisting of a single frequency laser, a 3 dB coupler, and waveguide photodiodes using a single epitaxial growth. A 3 GHz frequency modulated optical link was realized using this receiver.
Mode selection and transceiver design for rate maximization in underlay D2D MIMO systems (2015)

Linear coordinated transmit-receive beamforming methods are proposed for spatial underlay direct device-to-device (D2D) communication in cellular networks where both user terminals (UT) and base stations (BS) employ multiple antenna elements. For a D2D terminal pair, direct communication is a beneficial alternative compared to the cellular mode, where the direct data is relayed via BS. The transmitter and receiver design is formulated as a weighted sum-rate (WSR) maximization problem subject to individual transmit power constraints at BSs and users, where the utility is the aggregate sum of end-to-end data rates carried via uplink, downlink, and D2D links. The direct D2D links are allowed to co-exist with the cellular connections. The original problem is reformulated as an equivalent log-MSE minimization problem allowing alternating optimization of the transmit and receive beamformers. The precoder optimization step is efficiently solved using successive convex approximation (SCA) of the non-convex objective and constraints. According to the results, the system performance can be significantly improved with efficient mode selection between the BS and D2D transmission as opposed to solely serving all the users via D2D links or BS. Also, in certain scenarios, it is beneficial to allow a multi-route connection between the UTs.