gebhart/patrepeval huggingface dataset:
Computational Study of the Halogen Atom−Benzene Complexes (2003)

The structures of halogen atom-benzene complexes were investigated by modern DFT and ab initio computational methods. The spectroscopic properties of the complexes are also predicted and are in good agreement with experiment where such data have been reported. The fluorine atom-benzene complex is predicted to be a sigma complex due to the strength of a C-F bond. The chlorine atom-benzene complex is predicted to have an eta(1) pi complex structure, which is only slightly more favorable (1.1 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than a sigma complex but is significantly more stable (4.4 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than the eta(6) pi complex. The bromine and iodine benzene complexes are also predicted to prefer an eta(1) pi complex structure.
Toxicogenomic Response to Chlorination Includes Induction of Major Virulence Genes in Staphylococcus aureus (2007)

Despite the widespread use of chlorination for microbial control in aqueous environments, cellular response mechanisms of human pathogens, such as Staphylococcus aureus, against chlorination remain unknown. In this work, genome-wide transcriptional analysis was performed to elucidate cellular response of S. aureusto hypochlorous acid, an active antimicrobial product of chlorination in aqueous solution. Our results suggest that hypochlorous acid repressed transcription of genes involved in cell wall synthesis, membrane transport, protein synthesis, and primary metabolism, while amino acid synthesis genes were induced. Furthermore, hypochlorous acid induced transcription of genes encoding major virulence factors of S. aureus, such as exotoxins, hemolysins, leukocidins, coagulases, and surface adhesion proteins, which all play essential roles in staphylococcal virulence. This work implies that chlorination may stimulate production of virulence factors, which provides new insight into host-pathogen interactions and effects of chlorine application for microbial control.
Expression of high amounts of the CD117 molecule in a case of B-cell non-Hodgkin's lymphoma carrying the t(14:18) translocation (2000)

The c-kit proto-oncogen (CD117) has been described to be present in normal and neoplastic hemopoietic cells including both myeloid and lymphoid lineages. Among the normal lymphoid cells CD117 expression would be restricted to a small subset of NK-cells, and to early T-cell precursors and it is not expressed by normal B-cells. Regarding chronic lymphoproliferative disorders the only data provided up to now suggests that CD117 expression is restricted to cases of Hodgkin's disease and anaplastic large-cell lymphoma. In the present paper we describe a case of a B-cell chronic lymphoproliferative disorder carrying the t(14:18) translocation as demonstrated by molecular studies, in which the flow cytometric immunophenotypic analysis of both peripheral blood and bone marrow samples revealed the expression of high amounts of the CD117 antigen in the surface of the clonal B-cell population. Further studies are necessary to explore both the functional role of c-kit expression in the neoplastic B-cells from this patient and its potential utility for the diagnosis and follow-up of patients with B-cell non-Hodgkin's lymphoma.
Cloning specific segments of the mammalian genome: bacteriophage lambda containing mouse globin and surrounding gene sequences. (1977)

We have developed a general approach to the cloning of specific segments of the mammalian genome that involves a two-step purification of EcoRI fragments of mammalian DNA and their in vitro insertion into a suitably constructed EK2 derivative of bacteriophage lambda. The combination of fragment purification, exclusion of parental-type recombinants, and simple phage screening techniques permits the isolation of virtually any gene segment for which there is an identifying hybridization probe. We illustrate the approach by describing the cloning of an approximately 7000-base-long segment of mouse DNA containing globin and surrounding gene sequences.
Simultaneous data communication and position sensing with an impact ionization engineered avalanche photodiode array for free space optical communication (2017)

Photodetectors in free space optical communication systems perform two functions: reception of data communication signals and position sensing for pointing, tracking, and stabilization. Traditionally, the optical receive path in an FSO system is split into separate paths for data detection and position sensing. The need for separate paths is a consequence of conflicting performance criteria between position sensitive detectors (PSD) and data detectors. Combining the functionality of both detector types requires that the combinational sensor not only have the bandwidth to support high data rate communication but the active area and spatial discrimination to accommodate position sensing. In this paper we present a large area, concentric five element impact ionization engineered avalanche photodiode array rated for bandwidths beyond 1GHz with a measured carrier ionization ratio of less than 0.1 at moderate APD gains. The integration of this array as a combinational sensor in an FSO system is discussed along with the development of a pointing and stabilization algorithm.
Search for cognitive trait components of schizophrenia reveals a locus for verbal learning and memory on 4q and for visual working memory on 2q (2004)

Research to identify predisposing genes for complex diseases relying solely on clinical diagnosis is probably not ideal. Here, we analyzed genome-wide data for 168 schizophrenia families using neuropsychological variables associated with disease susceptibility, with the aid of SOLAR, a program for variance-component analysis. The linkage signal was greatly accentuated by application of the quantitative traits compared with diagnosis. We found evidence for a locus for verbal learning and memory on 4q21 (Z=3.01, Z(mp)=3.84 and empiric P=0.031 for delayed memory; Z=2.96, Z(mp)=3.4 and P=0.026 for verbal learning) and suggestive evidence for visual working memory on 2q36 (Z=2.80, Z(mp)=2.08 and P=0.093). In addition, some evidence emerged for a locus for recognition memory on 10p13, visual attention on 15q22 and executive function on 9p22 in the complete sample, as well as for delayed memory on 8q12, semantic clustering and intrusions on 1q42 and visual attention on 3p25 in the genealogically distinctive sample subsets. Of the loci linked to schizophrenia in diverse populations, in addition to the earlier mentioned regions, some evidence of linkage was observed for 2q, 6q, 7q, 11q, 13q, 14q, 18q and 22q. Our results reveal initial information on the effect of the loci associated with schizophrenia in multiple studies, and emphasize the value of trait components in the search for susceptibility loci for complex diseases.
Enhanced Mechanical Properties of Uniaxially Stretched Polylactide/Poly(ethylene oxide)-b-Poly(butylene oxide) Blend Films (2022)

Chain orientation, a natural consequence of polymer film processing, often leads to enhanced mechanical properties parallel to the machine extrusion direction (MD), while leaving the properties in the transverse direction (TD) unaffected or diminished, as compared to the unoriented material. Here, we report that mixing poly(ethylene oxide)-block-poly(butylene oxide) (PEO-PBO) diblock copolymer that forms dispersed particles in an amorphous polylactide (PLA) matrix produces uniaxially stretched blend films with enhanced toughness in both the MD and TD. Small-angle X-ray scattering experiments and visual observations revealed that the dominant deformation mechanism for blend films transitions from crazing to shear yielding in the MD as the stretching ratio increases, while crazing is the primary deformation mechanism in the TD at all stretching ratios investigated. As the films age at room temperature, crazing becomes more prevalent in the MD without compromising the improved toughness. The stretched blend films were susceptible to some degree of mechanical aging in the TD but remained fivefold tougher than stretched neat PLA films for up to 150 days. This work presents a feasible route to produce uniaxially stretched PEO–PBO/PLA films that are mechanically tough, which provides a more sustainable plastic alternative.
Drainage Canals in Southeast Asian Peatlands Increase Carbon Emissions (2021)

Abstract Drainage canals associated with logging and agriculture dry out organic soils in tropical peatlands, thereby threatening the viability of long‐term carbon stores due to increased emissions from decomposition, fire, and fluvial transport. In Southeast Asian peatlands, which have experienced decades of land use change, the exact extent and spatial distribution of drainage canals are unknown. This has prevented regional‐scale investigation of the relationships between drainage, land use, and carbon emissions. Here, we create the first regional map of drainage canals using high resolution satellite imagery and a convolutional neural network. We find that drainage is widespread—occurring in at least 65% of peatlands and across all land use types. Although previous estimates of peatland carbon emissions have relied on land use as a proxy for drainage, our maps show substantial variation in drainage density within land use types. Subsidence rates are 3.2 times larger in intensively drained areas than in non‐drained areas, highlighting the central role of drainage in mediating peat subsidence. Accounting for drainage canals was found to improve a subsidence prediction model by 30%, suggesting that canals contain information about subsidence not captured by land use alone. Thus, our data set can be used to improve subsidence and associated carbon emissions predictions in peatlands, and to target areas for hydrologic restoration.
Randomized Comparison of Antiarrhythmic Drug Therapy With Implantable Defibrillators in Patients Resuscitated From Cardiac Arrest (2000)

During long-term follow-up of cardiac arrest survivors, therapy with an ICD is associated with a 23% (nonsignificant) reduction of all-cause mortality rates when compared with treatment with amiodarone/metoprolol. The benefit of ICD therapy is more evident during the first 5 years after the index event.
Exogenous granulocyte–macrophage colony-stimulating factor promotes follicular development in the newborn rat in vivo (2005)

The present results suggest that GM-CSF may play a significant role in follicular development.
The design of expressive cartoons for the Web-Tinky (2003)

Tinky is a design environment which allows the generation, modification and animation of 3D cartoon-faces, where the face model is not based on a set of independent parameters that control specific abstract muscle emulations but is directed by a set of objects representing the elements of the face. In order to provide an easy to use authoring system producing standardised expressions and animations of Web oriented cartoons, we adopt an object oriented approach for cartoon design and combine it with the authoring qualities of VRML and the standardised set of facial and body animation parameters defined by MPEG-4 SNHC.
Supplementary Table 3B from Tumor Suppressor Functions of <i>ARLTS1</i> in Lung Cancers (2023)

Supplementary Table 3B from Tumor Suppressor Functions of &lt;i&gt;ARLTS1&lt;/i&gt; in Lung Cancers
Latency and network aware placement for cloud-native 5G/6G services (2022)

To meet ever more stringent requirements in terms of latency, 5G/6G networks are evolving from centralized to distributed architectures, for which the cloud-native paradigm with services decomposed into microservices is utmost relevant. This in turn raises the issue related to the distribution of network functions. In this paper, we introduce a novel microservice placement strategy considering the internal service composition, notably the communication between microservices. We formulate the placement as an optimization problem with the aim of minimizing end-to-end service latency. We solve the optimization problem with a combination of greedy and genetic algorithms.
Roles of Trp31 in High Membrane Binding and Proinflammatory Activity of Human Group V Phospholipase A2 (1999)

Group V phospholipase A2 is a recently discovered secretory phospholipase A2 (PLA2) that has been shown to be involved in eicosanoid formation in inflammatory cells, such as macrophages and mast cells. We have demonstrated that human group V PLA2 (hsPLA2-V) can bind phosphatidylcholine (PC) membranes and hydrolyze PC substrates much more efficiently than human group IIa PLA2, which makes it better suited for acting on the outer plasma membrane (Han, S.-K., Yoon, E. T., and Cho, W. (1998) Biochem. J. 331, 353-357). In this study, we demonstrate that exogenous hsPLA2-V has much greater activity than does group IIa PLA2 to release fatty acids from various mammalian cells and to elicit leukotriene B4 formation from human neutrophils. To understand the molecular basis of these activities, we mutated two surface tryptophans of hsPLA2-V to alanine (W31A and W79A) and measured the effects of these mutations on the kinetic activity toward various substrates, on the binding affinity for vesicles and phospholipid-coated beads, on the penetration into phospholipid monolayers, and on the activity to release fatty acids and elicit eicosanoid formation from various mammalian cells. These studies show that the relatively high ability of hsPLA2-V to induce cellular eicosanoid formation derives from its high affinity for PC membranes and that Trp31 on its putative interfacial binding surface plays an important role in its binding to PC vesicles and to the outer plasma membrane.
Vagal stimulation in brain dead donor rats decreases chronic allograft nephropathy in recipients (2013)

In conclusion, our data demonstrate a long-lasting beneficial effect of vagus nerve stimulation in BD donors on the renal transplantation outcome. Hence, activation of the cholinergic anti-inflammatory pathway in BD donors may represent a novel therapeutic modality to reduce chronic allograft nephropathy without any side effects for the recipient.
ChemInform Abstract: Design of Functional Nucleic Acid Systems for Biomolecular Analysis (2011)

Abstract Review: 55 refs.
Automated Parallel Synthesis in Support of Early Drug Discovery: Balancing Accessibility of Chemistry with the Design of Drug-Like Libraries (2007)

Automated parallel synthesis provides chemistry muscle to early-stage drug discovery programs enabling the efficient and comprehensive exploration of desirable chemistry space. A discovery strategy that involves the high-throughput screening of a compound collection with a parallel synthesis heritage will fuel the rapid expansion of SAR from validated chemical procedures. This approach, however, relies heavily on the accessibility of synthetic methods to prepare the molecules of interest. Combinatorial chemistry techniques have been plagued with the challenge of developing methods for the synthesis of the right compounds and not just those that are chemically feasible. This formidable obstacle can be overcome only by integrating multiple disciplines and technologies. Herein, we provide details of our approach with applications in support of drug discovery programs.
Rates of Convergence of Performance Gradient Estimates Using Function Approximation and Bias in Reinforcement Learning (2001)

We address two open theoretical questions in Policy Gradient Reinforcement Learning. The first concerns the efficacy of using function approximation to represent the state action value function, Q. Theory is presented showing that linear function approximation representations of Q can degrade the rate of convergence of performance gradient estimates by a factor of O(ML) relative to when no function approximation of Q is used, where M is the number of possible actions and L is the number of basis functions in the function approximation representation. The second concerns the use of a bias term in estimating the state action value function. Theory is presented showing that a non-zero bias term can improve the rate of convergence of performance gradient estimates by O(1 (1/M)), where M is the number of possible actions. Experimental evidence is presented showing that these theoretical results lead to significant improvement in the convergence properties of Policy Gradient Reinforcement Learning algorithms.
Reflections After 50-Plus Years in the Classroom [Reflections] (2021)

Our field has had a rich history, and clearly it has incredible potential going forward. There is always an opportunity for discovering or rediscovering mathe-matical principles that have not yet been fully exploited in the context of signal processing. And physics will continue to provide us with new ways of imple-menting signal processing systems. While digital platforms have played an increasingly important part in signal processing system implementation, the role of analog platforms also continues to grow, as does a mix of both. And quite likely, as the technology advances,it will become increasingly difficult to define precisely which parts of a sys-tem are considered analog and which are digital.
Dual Neural Network Architecture for Determining Permeability and Associated Uncertainty (2021)

The computation of permeability is vital for reservoir characterization because it is a key parameter in the reservoir models used for estimating and optimizing hydrocarbon production. Permeability is routinely predicted as a correlation from near-wellbore formation properties measured through wireline logs. Several such correlations, namely Schlumberger-Doll Research (SDR) permeability and Timur-Coates permeability models using nuclear magnetic resonance (NMR) measurements, K-lambda using mineralogy, and other variants, have often been used, with moderate success. In addition to permeability, the determination of the uncertainties, both epistemic (model) and aleatoric (data), are important for interpreting variations in the predictions of the reservoir models. In this paper, we demonstrate a novel dual deep neural network framework encompassing a Bayesian neural network (BNN) and an artificial neural network (ANN) for determining accurate permeability values along with associated uncertainties. Deep-learning techniques have been shown to be effective for regression problems but quantifying the uncertainty of their predictions and separating them into the epistemic and aleatoric fractions is still considered challenging. This is especially vital for petrophysical answer products because these algorithms need the ability to flag data from new geological formations that the model was not trained on as “out of distribution” and assign them higher uncertainty. Additionally, the model outputs need sensitivity to heteroscedastic aleatoric noise in the feature space arising due to tool and geological origins. Reducing these uncertainties is key to designing intelligent logging tools and applications, such as automated log interpretation. In this paper, we train a BNN with NMR and mineralogy data to determine permeability with associated epistemic uncertainty, obtained by determining the posterior weight distributions of the network by using variational inference. This provides us the ability to differentiate in- and out-of-distribution predictions, thereby identifying the suitability of the trained models for application in new geological formations. The errors in the prediction of the BNN are fed into a second ANN trained to correlate the predicted uncertainty to the error of the first BNN. Both networks are trained simultaneously and therefore optimized together to estimate permeability and associated uncertainty. The machine-learning permeability model is trained on a “ground-truth” core database and demonstrates considerable improvement over traditional SDR and Timur-Coates permeability models on wells from the Ivar Aasen Field. We also demonstrate the value of information (VOI) of different logging measurements by replacing the logs with their median values from nearby wells and studying the increase in the mean square errors.
Inter-symbol Interference in High Data Rate UWB Communications Using Energy Detector Receivers (2006)

Inter-symbol interference (ISI) is known to be a major factor complicating the realization of high data rate ultrawideband (UWB) communications. In the literature, methods for suppressing ISI in UWB systems employing complex receivers exist. In this paper, considering the low cost requirement along with the need for high data rates, we propose a modified, on-off keying (OOK) based low complexity energy detector receiver capable of eliminating ISI. The presented receiver utilizes an ISI cancellation algorithm depending on decision feedback equalization (DFE) and it is advantageous in that it does not suffer from error propagation. The results obtained demonstrate a considerable gain in the symbol detection performance of the UWB system.
Effect of PF-00547659 on Central Nervous System Immune Surveillance and Circulating β7+ T Cells in Crohn’s Disease: Report of the TOSCA Study (2017)

In patients with active Crohn's disease, natalizumab therapy increases the risk for PML, and the increased risk is thought to be associated with iatrogenic leukopenia within the CNS. PML under PF-00547659 may be a lesser concern, as this agent did not reduce lymphocytes or T cell subsets in the cerebrospinal fluid.
Intrazeolite topotaxy: sodium-23 double-rotation NMR study of transition-metal hexacarbonyls and oxides encapsulated in sodium zeolite Y. [Erratum to document cited in CA117(4):34240c] (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleIntrazeolite topotaxy: sodium-23 double-rotation NMR study of transition-metal hexacarbonyls and oxides encapsulated in sodium zeolite Y. [Erratum to document cited in CA117(4):34240c]Raz Jelinek, Saim Ozkar, Geoffrey A. Ozin, and Heloise O. PastoreCite this: J. Phys. Chem. 1992, 96, 23, 9582Publication Date (Print):November 1, 1992Publication History Published online1 May 2002Published inissue 1 November 1992https://doi.org/10.1021/j100202a094RIGHTS & PERMISSIONSArticle Views15Altmetric-Citations6LEARN 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 InReddit PDF (85 KB) Get e-Alerts