gebhart/patrepeval huggingface dataset:
Antisense oligodeoxynucleotide phosphorothioate complementary to Gag mRNA blocks replication of human immunodeficiency virus type 1 in human peripheral blood cells. (1994)

Gene-expression modulator 91 (GEM91) is a 25-nt antisense oligodeoxynucleotide phosphorothioate complementary to the Gag mRNA of human immunodeficiency virus type 1 (HIV-1). Cellular uptake and intracellular distribution of GEM91 within cells suggest that this oligomer is readily available for antisense activity. GEM91 inhibited HIV-1 replication in a dose-dependent and sequence-specific manner. In a comparative study, 2 microM GEM91 was as effective as 5 microM 3'-azido-3'-deoxythymidine in blocking virus replication during the 28-day treatment of an HIV-1-infected T-cell line. GEM91 also completely inhibited (> 99%) the growth of three different HIV-1 isolates in primary lymphocytes and prevented the cytopathic effect of the virus in primary CD4+ T cells. Similarly, treatment with GEM91 for 3 weeks of HIV-1/BaL-infected primary macrophages blocked virus replication. Based on GEM91 anti-HIV-activity, safety, and pharmacokinetic profile in animals, a clinical trial was started using this compound as an antisense oligonucleotide drug for the treatment of the acquired immunodeficiency syndrome.
Simulated imaging of atherosclerotic & radiofrequency ablation lesions using phase subtraction (2015)

Cardiovascular diseases are the main cause of death worldwide. Atherosclerosis and atrial fibrillation are structural and electrical pathophysiology, respectively, that can lead to acute events such as stroke or myocardial infarction. We used particle-based Monte Carlo methods to simulate X-ray phase imaging of atherosclerotic plaque types IV-VIII in the aorta, iliac, and coronary arteries. We also assessed scar lesion development in radiofrequency catheter ablation treatment of atrial fibrillation by simulating lesions 2, 5, 10, 30, and 60 days post-procedure. For both applications, we found high signal-to-noise and contrast-to-noise ratios in all lesions. These results suggest that X-ray phase imaging is a viable technique for non-invasive quantitative cardiovascular lesion characterization.
A soft pairing approach for MUROS to increase voice capacity in GERAN (2010)

In GERAN networks, Multiple Users Reusing One Single timeslot (MUROS) promises to enhance the cell capacity through pairing of two or more users onto a single timeslot. So far no work has been done on the basis on which the different users would be paired. The criteria used for the pairing decision to pair two or more users is critical for MUROS as this will eventually decide the actual gains due to MUROS. Currently there exists no work that has evaluated pairing criteria or the system impacts of pairing decision process in MUROS. When pairing two or more users, care should be taken that the link quality of the two or more users being paired does not see a drastic degradation leading to call drops. In this paper a novel soft pairing approach is suggested. The gains provided by the Soft Pairing approach are presented through system simulations. We also formulate the problem of pairing in MUROS in a game theoretic setting to better understand the system level impact of trying to maximize paired users in a cell and over all system throughput.
Prevention of Hematite Settling in Water-Based Mud at High Pressure and High Temperature (2021)

Hematite was recently introduced as a weighting agent in drilling fluids; however, its use has some problems because of the settlement of solid particles (solid sagging). Particularly when it comes to high-pressure high-temperature (HP/HT) wells, sagging causes inconsistency in the drilling fluid and gives rise to serious drilling operational and technical challenges. This work provides a solution to this challenge via a thorough investigation of hematite sagging in water-based mud for HP/HT applications where ilmenite is combined with hematite. The particles of both hematite and ilmenite were first characterized to address their mineralogical and textural features. Field mud formulation was employed using several ilmenite/hematite contents (i.e., 0/100, 25/75, and 50/50% ilmenite/hematite). Then, laboratory experiments were conducted to study the density, pH, and sag performance of the produced drilling fluids. From the sagging tests, the optimal ilmenite/hematite ratio was determined, and rheology, viscoelastic behavior, and filtration properties of the formulated mud were addressed. The tests were conditioned to 300 psi and 250 °F. The results showed a reduction in mud density and pH with increasing ilmenite content, as the density reduced from15 ppg with base hematite until 14.2 ppg for the 50% ilmenite mixture and the pH reduced from 10.5 to 9.3. The static and dynamic sag tests indicated that the addition of 25% of ilmenite solved the hematite-incorporated sagging issue by well placing the sag tendency within the recommended safe range. The 25/75% combination enhanced the yield point (YP) by 37% with only 1 cP increment in plastic viscosity (PV) and an insignificant effect on the gel strength. The YP/PV ratio was improved by 31% indicating better hole cleaning and solid suspension. The filtration behavior of the 25% ilmenite mixture was superior compared to that of the blank hematite because it resulted in 35, 39, and 35% reduction in the filtrate volume, filter-cake weight, and thickness, respectively. This work contributes to improving and economizing the drilling cost and time by the formulation of a stabilized and distinguished-performance drilling mud using combined weighting agents at HP/HT.
A Generic Solution to Integrate SQL and Analytics for Big Data (2015)

There is a need to integrate SQL processing with more advanced machine learning (ML) analytics to drive actionable insights from large volumes of data. As a first step towards this integration, we study how to efficiently connect big SQL systems (either MPP databases or new-generation SQL-on-Hadoop systems) with distributed big ML systems. We identify two important challenges to address in the integrated data analytics pipeline: data transformation, how to efficiently transform SQL data into a form suitable for ML, and data transfer, how to efficiently handover SQL data to ML systems. For the data transformation problem, we propose an In-SQL approach to incorporate common data transformations for ML inside SQL systems through extended user-defined functions (UDFs), by exploiting the massive parallelism of the big SQL systems. We propose and study a general method for transferring data between big SQL and big ML systems in a parallel streaming fashion. Furthermore, we explore caching intermediate or final results of data transformation to improve the performance. Our techniques are generic: they apply to any big SQL system that supports UDFs and any big ML system that uses Hadoop InputFormats to ingest input data.
The PTI ‐suppressing Avr2 effector from Fusarium oxysporum suppresses mono‐ubiquitination and plasma membrane dissociation of BIK1 (2023)

Plant pathogens use effector proteins to target host processes involved in pathogen perception, immune signalling, or defence outputs. Unlike foliar pathogens, it is poorly understood how root-invading pathogens suppress immunity. The Avr2 effector from the tomato root- and xylem-colonizing pathogen Fusarium oxysporum suppresses immune signalling induced by various pathogen-associated molecular patterns (PAMPs). It is unknown how Avr2 targets the immune system. Transgenic AVR2 Arabidopsis thaliana phenocopies mutants in which the pattern recognition receptor (PRR) co-receptor BRI1-ASSOCIATED RECEPTOR KINASE (BAK1) or its downstream signalling kinase BOTRYTIS-INDUCED KINASE 1 (BIK1) are knocked out. We therefore tested whether these kinases are Avr2 targets. Flg22-induced complex formation of the PRR FLAGELLIN SENSITIVE 2 and BAK1 occurred in the presence and absence of Avr2, indicating that Avr2 does not affect BAK1 function or PRR complex formation. Bimolecular fluorescence complementation assays showed that Avr2 and BIK1 co-localize in planta. Although Avr2 did not affect flg22-induced BIK1 phosphorylation, mono-ubiquitination was compromised. Furthermore, Avr2 affected BIK1 abundance and shifted its localization from nucleocytoplasmic to the cell periphery/plasma membrane. Together, these data imply that Avr2 may retain BIK1 at the plasma membrane, thereby suppressing its ability to activate immune signalling. Because mono-ubiquitination of BIK1 is required for its internalization, interference with this process by Avr2 could provide a mechanistic explanation for the compromised BIK1 mobility upon flg22 treatment. The identification of BIK1 as an effector target of a root-invading vascular pathogen identifies this kinase as a conserved signalling component for both root and shoot immunity.
Synthesis, Characterization, and Catalytic Reactivities of Novel Dinuclear Cu(II) Complexes : Efficient Ring Opening Reaction of Epoxide (2023)

Abstract Novel tridentate N 2 O‐type ligands L1 – L4 (((((X‐benzyl)pyridine‐2‐yl)methylamino)methyl)phenol); L1 for X=4‐CH 3 , L2 for X=H, L3 for X=2‐F, L4 for X=4‐CF 3 ) and their dinuclear copper(II) complexes C1 – C4 ( C1 for [( L1 ) 2 Cu 2 (NO 3 ) 2 ], C2 for [( L2 ) 2 Cu 2 (NO 3 ) 2 ], C3 for [( L3 ) 2 Cu 2 (NO 3 ) 2 ] and C4 for [( L4 ) 2 Cu 2 (NO 3 ) 2 ]) was synthesized and verified by 1 H NMR, IR, and ESI‐Mass. The structural forms of the copper complexes were determined by X‐ray crystallography. The dinuclear copper complexes C1 – C4 showed efficient ring‐opening properties of epoxides with methanol under mild conditions. In particular, the copper complex C1 having electron‐donating group in the ligand showed the most efficient reactivity in the ring opening of epoxides. The sole attack at the benzylic carbon of styrene oxide and the less steric preference in 1,2‐epoxyhexane demonstrated that the regiochemistry of the ring opening catalyzed by dinuclear copper complexes might be dependent on the electronic feature of epoxide.
Suppression of Hepcidin Expression and Iron Overload Mediate Salmonella Susceptibility in Ankyrin 1 ENU-Induced Mutant (2013)

Salmonella, a ubiquitous Gram-negative intracellular bacterium, is a food borne pathogen that infects a broad range of hosts. Infection with Salmonella Typhimurium in mice is a broadly recognized experimental model resembling typhoid fever in humans. Using a N-ethyl-N-nitrosurea (ENU) mutagenesis recessive screen, we report the identification of Ity16 (Immunity to Typhimurium locus 16), a locus responsible for increased susceptibility to infection. The position of Ity16 was refined on chromosome 8 and a nonsense mutation was identified in the ankyrin 1 (Ank1) gene. ANK1 plays an important role in the formation and stabilization of the red cell cytoskeleton. The Ank1(Ity16/Ity16) mutation causes severe hemolytic anemia in uninfected mice resulting in splenomegaly, hyperbilirubinemia, jaundice, extramedullary erythropoiesis and iron overload in liver and kidneys. Ank1(Ity16/Ity16) mutant mice demonstrated low levels of hepcidin (Hamp) expression and significant increases in the expression of the growth differentiation factor 15 (Gdf15), erythropoietin (Epo) and heme oxygenase 1 (Hmox1) exacerbating extramedullary erythropoiesis, tissue iron deposition and splenomegaly. As the infection progresses in Ank1(Ity16/Ity16), the anemia worsens and bacterial load were high in liver and kidneys compared to wild type mice. Heterozygous Ank1(+/Ity16) mice were also more susceptible to Salmonella infection although to a lesser extent than Ank1(Ity16/Ity16) and they did not inherently present anemia and splenomegaly. During infection, iron accumulated in the kidneys of Ank1(+/Ity16) mice where bacterial loads were high compared to littermate controls. The critical role of HAMP in the host response to Salmonella infection was validated by showing increased susceptibility to infection in Hamp-deficient mice and significant survival benefits in Ank1(+/Ity16) heterozygous mice treated with HAMP peptide. This study illustrates that the regulation of Hamp and iron balance are crucial in the host response to Salmonella infection in Ank1 mutants.
A Potential–dependent Thiele Modulus to Quantify the Effectiveness of Porous Electrocatalysts (2021)

&lt;p&gt;Electrochemical reactors often employ high surface area electrocatalysts to accelerate volumetric reaction rates and increase productivity. While electrocatalysts can alleviate kinetic overpotentials, diffusional resistances at the pore-scale often prevent full catalyst utilization. The effect of intraparticle diffusion on the overall reaction rate can be quantified through an effectiveness factor expression governed by the Thiele modulus parameter. This analytical approach is integral to the development of catalytic structures for thermochemical processes and can be extended to electrochemical processes provided the relationship between reaction kinetics and electrode overpotential is incorporated. Here, we derive a potential-dependent Thiele modulus to quantify the effectiveness factor for porous electrocatalytic structures. We apply this mathematical framework to spherical microparticles as a function of applied overpotential across catalyst properties and reactant characteristics. The relative effects of kinetics and mass transport are related to overall reaction rates, revealing markedly lower catalyst utilization at increasing overpotential. Subsequently, we generalize the analysis to alternative catalyst shapes and provide guidance on the design of porous catalytic materials for use in electrochemical reactors.&lt;/p&gt;
Neonatal hematological parameters and the risk of moderate-severe bronchopulmonary dysplasia in extremely premature infants (2019)

Our findings suggest that hematologic parameters at birth are different in extremely preterm infants who will develop moderate-severe BPD. A higher platelet count at birth may increase the risk of moderate-severe BPD after extremely premature birth.
Novel natural supplement for the production of fungal cellulases and application for enzymatic saccharification of wheat straw (2015)

The cost effective production of cellulolytic enzymes and their use for generating higher reducing sugars from lignocellulosic biomass is critical for attaining the commercial viability of lignocellulosic biofuels production. Optimizing the use of locally available agroresidues and natural nutritional alternatives for fungal growth and enzyme production can reduce the cost of enzyme production. In the present work, maximum cellulolytic activity of 30.85 IU/gds was obtained from Trichoderma reesei NCIM 1186 using wheat bran as the substrate and coconut water as the nutritional supplement. The produced cellualse was used for enzymatic saccharification of phosphoric acid pretreated wheat straw. The enzymatic sachharification was optimized through central composite design (CCD) based response surface methodology (RSM). Maximum reducing sugar yields of 371.44 mg/g dry substrate were obtained at 18% (w/v) substrate concentration, 50°C and 24 h of incubation time. Further, the saccharified sugar hydrolysate was fermented using S . cerevisiae NCIM 3215. Maximum ethanol production (2.58% w/v) obtained after 24 h of fermentation at 30°C. © 2015 American Institute of Chemical Engineers Environ Prog, 34: 1243–1248, 2015
Resonance Assignments for Solid Peptides by Dipolar-Mediated 13C/15N Correlation Solid-State NMR (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTResonance Assignments for Solid Peptides by Dipolar-Mediated 13C/15N Correlation Solid-State NMRMei Hong and Robert G. GriffinView Author Information Francis Bitter Magnet Laboratory and Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139 Cite this: J. Am. Chem. Soc. 1998, 120, 28, 7113–7114Publication Date (Web):July 1, 1998Publication History Received9 March 1998Published online1 July 1998Published inissue 1 July 1998https://pubs.acs.org/doi/10.1021/ja980775whttps://doi.org/10.1021/ja980775wrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views450Altmetric-Citations112LEARN 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 SUBJECTS:Carbon,Carbonyls,Peptides and proteins,Quantum mechanics,Resonance structures Get e-Alerts
Surgical Strategies for Combined Hepatocellular-Cholangiocarcinoma (cHCC-CC) (2023)

Combined hepatocellular-cholangiocarcinoma (cHCC-CC) is a tumor entity presenting features of hepatocellular and cholangiocellular epithelial differentiation. Due to the likeness between cHCC-CC, HCC and CC, accurate pretherapeutical diagnosis is challenging and advanced stages are prevalent. Radical oncological surgery is the only curative therapeutical option in patients with cHCC-CC. To reach this goal a profound understanding of this rare liver tumor is crucial. Factors such as clinicopathological characteristics, growth patterns and biological behavior are of central importance. To explore onco-surgical strategies and aspects for complete resection of cHCC-CC and to answer important key questions, an extensive review of the literature was conducted to answer the following questions: What are the best surgical options? Is there a significance for nonanatomical resections? Is there a prognostic value of concomitant lymphadenectomy? What about multimodal concepts in local advanced cHCC-CC? The role of minimally invasive liver surgery (MILS) including the role of robotic liver surgery for cHCC-CC will be discussed. While liver transplantation (LT) is standard for patients with unresectable HCC, the role of LT in cHCC-CC patients is still controversial. How can patients with high risk for early tumor recurrence be identified to avoid aggressive surgical treatment without clinical benefit? The comprehensive understanding of this challenging liver tumor will help to improve future treatment options for these patients.
Imatinib Mesylate (Gleevec®) Is Active in Relapsed/Refractory Waldenstrom’s Macroglobulinemia: Planned Interim Results of WMCTG Clinical Trial 05-140. (2006)

Abstract Waldenstrom’s macroglobulinemia is a B-cell disorder characterized by the infiltration of lymphoplasmacytic cells (LPC) in the bone marrow (BM), along with an IgM monoclonal gammopathy. Characteristic of WM is an increased number of mast cells (MC) which are found in association with LPC, and stimulate LPC growth through several TNF-family members including CD40L, APRIL and BLYS (Ann Oncol17:1275; Blood104:917A). As such, we have targeted MC in WM. One important growth and survival factor for MC is stem cell factor (SCF), which signals through CD117. Imatinib mesylate blocks SCF signaling through CD117, and induces apoptosis of WM BM MC and LPC, both of which highly express CD117 (Blood2004; 104:314b). As such, we performed this Phase II study of imatinib mesylate in patients with relapsed and refractory WM. Intended therapy consisted of imatinib mesylate which was initiated at 400 mg po qD over the first month, and subsequently dose escalated to 600 mg po qD for up to 2 years. Dose de-escalation to 300 mg po qD was permitted for toxicity. Thirteen patients were enrolled and are eligible for evaluation at interim analysis. Median age was 64 (range 53–80 years), and median prior therapies was 2 (range 1–5). Nine and four patients had relapsed and refractory disease, respectively. Following a median of 3 months of therapy, median serum IgM levels for all evaluable patients declined from 3190 (range 763–8130 mg/dL) to 2095 (range 695–7340 mg/dL) at best response (p=0.009). On an intent to treat analysis, 6/13 (46.2%) of patients attained a ≥25% decrease in serum IgM. Responses were prompt, and occurred at a median of 2.5 months. Overall, therapy was well tolerated with ≥grade 2 toxicities as follows: anemia (n=4); edema (n=3); hyperglycemia (n=2); leukopenia (n=2); thrombocytopenia (n=1); neutropenia (n=1); and resulted for 4 patients in dose modification (n=4) or treatment cessation (n=3). The interim results of this study demonstrate that imatinib mesylate is an active and well-tolerated salvage therapy for WM.
Communication Limits with Low Precision Analog-to-Digital Conversion at the Receiver (2007)

We examine the Shannon limits of communication systems when the precision of the analog-to-digital conversion (ADC) at the receiver is constrained. ADC is costly and power- hungry at high speeds, hence ADC precision is expected to be a limiting factor in the performance of receivers which are heavily based on digital signal processing. In this paper, we consider transmission over an ideal discrete-time real baseband additive white Gaussian noise (AWGN) channel, and provide capacity results when the receiver ADC employs a small number of bits, generalizing our prior work on one bit ADC. We show that dithered ADC does not increase capacity, and hence restrict attention to deterministic quantizers. To compute the capacity, we use a dual formulation of the channel capacity problem, which is attractive due to the discrete nature of the output alphabet. The numerical results we obtain strongly support our conjecture that the optimal input distribution is discrete, and has at most one mass point in each quantizer interval. This implies, for example, that it is not possible to support large alphabets such as 64-QAM using 2-bit quantization on the I and Q channels, at least with symbol rate sampling.
Nucleophilic Addition to 3‐Substituted Pyridinium Salts: Expedient Syntheses of (‐)‐L‐733,061 and (‐)‐CP‐99,994. (2004)

The addition of nucleophiles to 3-substituted pyridinium salts prepared from &lt;i&gt;N&lt;/i&gt;-methylbenzamide and various pyridines has been investigated.\nGood to excellent regioselectivities favoring the 2,3-disubstituted 1,2-dihydropyridines were observed. The resulting 1,2-dihydropyridines led\nto the corresponding 2,3-disubstituted pyridines upon treatment with Mn(OAc)&lt;sub&gt;3&lt;/sub&gt;/NaIO&lt;sub&gt;4&lt;/sub&gt;. This methodology was also successfully applied to the\nenantioselective syntheses of (−)-L-733,061 and (−)-CP-99,994, two members of a new class of highly potent, nonpeptide, Substance P antagonists.
Privately Detecting Pairwise Correlations in Distributed Time Series (2011)

In this paper, we propose developing a generic framework for privately identifying similarities or correlations within and/or across basic statistics, e.g. mean, for independently owned, distributed participant data. To obscure the actual statistical values and improve the levels of privacy, we propose using scaled bin values instead of raw data. We find that while there is a natural trade off between privacy and accuracy, we can maintain reasonable correlation accuracy across different levels of privacy and different adversarial backgrounds for time series data with varying distributions.