gebhart/patrepeval huggingface dataset:
Activity of acid deoxyribonuclease towards diastereoisomers of thymidyl 3'-(4-nitrophenyl phosphorothioate). Stereochemistry of transnucleotidylation reaction. (1986)

The (Rp)- and (Sp)-diastereoisomers of thymidyl 3'-(4-nitrophenyl phosphorothioate) (1) were found to act as unusual substrates for acid deoxyribonuclease (DNase II). Instead of the expected thymidine 3'-phosphorothioate, the product resulting from the reaction of (Rp)-1 catalyzed by DNase II was identified as (Sp, Rp)-thymidyl (3'-5')thymidyl phosphorothioate 3'-(4-nitrophenyl phosphorothioate), while that from (Sp)-1 has been recognized as a 10:1 mixture of (Sp, Rp)-thymidyl (3'-5')thymidyl phosphorothioate 5'-(4-nitrophenyl phosphorothioate) and (Rp, Sp)-thymidyl (3'-5')-thymidyl phosphorothioate 3'-(4-nitrophenyl phosphorothioate), respectively. Both types of transnucleotidylations were found to occur with retention of configuration at phosphorus. Stereochemical results may be interpreted in terms of two step mechanisms involving the formation of the intermediate, covalent substrate enzyme complexes.
Methane Reforming with Carbon Dioxide and Oxygen under Atmospheric and Pressurized Conditions Using Fixed- and Fluidized-Bed Reactors (2002)

Effect of the reactor in methane reforming with carbon dioxide and oxygen over NiO-MgO catalysts under atmospheric and pressurized conditions was investigated. Under atmospheric pressure, the stable activity was observed using the fluidized bed reactor. However, in the fixed bed reactor, the activity decreased gradually with time on stream. On the other hand, at low temperature and high space velocity, methane conversion decreased rapidly to the level of methane combustion using fluidized bed reactor. Under pressurized condition, the stable production of syngas was possible even at high space velocity since the catalyst is in more reducing atmosphere at higher pressure. The fluidized bed reactor enhanced more effective conversion of methane to syngas than the fixed bed reactor.
The future of microwork (2016)

What happens when we algorithmically break complex productivity tasks down into microtasks? At Microsoft Research, the author and her team are accelerating a shift toward microproductivity to make it easy for people to get big things done one small step at a time.
Manipulating a spin qubit by the backaction of sequential partial adaptive measurements (2014)

We report the control-free manipulation of a nuclear spin qubit in diamond, using only the backaction of sequential partial measurements with real-time feedback.
A UWB transmit-only based scheme for multi-tag support in a millimeter accuracy localization system (2013)

Ultra Wideband (UWB) wireless positioning systems have many advantages for tracking and locating items in indoor environments. Surgical navigation and industrial process control are potential applications for high accuracy UWB localization systems with millimeter accuracy. Several experimental systems have achieved very high accuracy, but have generally neglected significant system features like multi-tag access. This paper outlines a UWB localization system, which addresses both multi-tag performance and localization accuracy using UWB transmit-only digital communication and time difference of arrival (TDOA). The scheme takes advantage of a digital sampling circuit that can be used for both sub-sampling and data reception. Preliminary 1-D experimental results using this system resulted in a total system update rate of 889 Hz and localization accuracy of 3.25mm.
GSM video communication (2003)

We propose a novel enhanced wireless hypercompressed video surveillance system for advanced warning of such threats as asymmetric threats from terrorist attacks. A novel video interface card (VIC) technology is proposed for transmitting spatial and temporal events with very low GSM (9.6kbps) bandwidth, in spite of high original VGA-video bandwidth (221 Mbps).
Discovery of Danoprevir (ITMN-191/R7227), a Highly Selective and Potent Inhibitor of Hepatitis C Virus (HCV) NS3/4A Protease (2013)

HCV serine protease NS3 represents an attractive drug target because it is not only essential for viral replication but also implicated in the viral evasion of the host immune response pathway through direct cleavage of key proteins in the human innate immune system. Through structure-based drug design and optimization, macrocyclic peptidomimetic molecules bearing both a lipophilic P2 isoindoline carbamate and a P1/P1' acylsulfonamide/acylsulfamide carboxylic acid bioisostere were prepared that possessed subnanomolar potency against the NS3 protease in a subgenomic replicon-based cellular assay (Huh-7). Danoprevir (compound 49) was selected as the clinical development candidate for its favorable potency profile across multiple HCV genotypes and key mutant strains and for its good in vitro ADME profiles and in vivo target tissue (liver) exposures across multiple animal species. X-ray crystallographic studies elucidated several key features in the binding of danoprevir to HCV NS3 protease and proved invaluable to our iterative structure-based design strategy.
Tracing data errors with view-conditioned causality (2011)

A surprising query result is often an indication of errors in the query or the underlying data. Recent work suggests using causal reasoning to find explanations for the surprising result. In practice, however, one often has multiple queries and/or multiple answers, some of which may be considered correct and others unexpected. In this paper, we focus on determining the causes of a set of unexpected results, possibly conditioned on some prior knowledge of the correctness of another set of results. We call this problem View-Conditioned Causality. We adapt the definitions of causality and responsibility for the case of multiple answers/views and provide a non-trivial algorithm that reduces the problem of finding causes and their responsibility to a satisfiability problem that can be solved with existing tools. We evaluate both the accuracy and effectiveness of our approach on a real dataset of user-generated mobile device tracking data, and demonstrate that it can identify causes of error more effectively than static Boolean influence and alternative notions of causality.
Comparison of combinations of interferons with tumor specific and nonspecific monoclonal antibodies as therapy for murine B- and T-cell lymphomas. (1988)

Two murine models, C3H 38C13 B-cell lymphoma and AKR SL2 T-cell lymphoma were used to determine the efficacy of three different interferon preparations, recombinant human hybrid interferon-alpha A/D, recombinant murine interferon (rMIFN)-gamma, and natural MIFN-alpha/beta (greater than or equal to 85% beta), alone and in combination with tumor specific and nonspecific monoclonal antibody therapy. All three interferon preparations have direct in vitro antigrowth activity for 38C13 and SL2. All three interferons have direct antitumor activity in vivo for 38C13 lymphoma at high doses; however, none of these interferons has independent antitumor activity for SL2 in vivo. These data indicate that there is no relationship between in vitro growth cytostasis/cytolysis and in vivo antitumor response. All three interferon preparations will potentiate both tumor specific and nonspecific monoclonal antibody therapy. Natural MIFN-alpha/beta and recombinant human hybrid interferon-alpha A/D, which should share a common cell surface receptor, had similar antitumor activity in both models. Combining recombinant human hybrid interferon-alpha A/D and rMIFN-gamma therapy was not additive for 38C13 lymphoma and a three-way combination with antiidiotype was not significantly more effective than combination therapy with one interferon type. In general, rMIFN-gamma was more effective in in vivo combination therapy against the s.c. T-cell lymphoma than against the i.p. B-cell lymphoma and was more synergistic with anti-Thy1.1 than with antiidiotype.
Nanostructured carbon electrodes for energy storage (2010)

Current work on using nanostructured carbon surfaces in supercapacitors and batteries to enable enhanced performance is discussed. The emphasis is on solid electrolyte based batteries and supercapacitors which can be flexible and change form factor. This is a new concept for energy storage systems driven by the requirements of next generation mobile communication devices which will be designed to supplement regular battery power with power from harvested energy. It will be shown that a new class of flexible supercapacitors and batteries can be realised through use of carbon electrodes with enhanced nanostructure. In particular Carbon nanohons (CNH) are considered. CNHs are formed in 'crushed' or 'origami -like' graphene sheets. They form into 10 -50 nm diameter particles with a high degree of open pores having high surface area and permeability. The variable spacing between 5nm -lnm of two graphene sheets in CNH introduces a new surface energy regime for intercollation of ions. Results from applying CNH in electrodes in supercapacitors and batteries are presented. The power density of a flexible supercapacitor, for example, can be increased very significantly by designing nanostructure into the carbon electrodes. The devices under consideration are aimed at powering mobile electronic and autonomous sensing systems. However, the potential of scaling of the technology to larger energy storage systems is viable.
Regulation of the cystic fibrosis transmembrane conductance regulator anion channel by tyrosine phosphorylation (2015)

The cystic fibrosis transmembrane conductance regulator (CFTR) channel is activated by PKA phosphorylation of a regulatory domain that interacts dynamically with multiple CFTR domains and with other proteins. The large number of consensus sequences for phosphorylation by PKA has naturally focused most attention on regulation by this kinase. We report here that human CFTR is also phosphorylated by the tyrosine kinases p60c-Src (proto-oncogene tyrosine-protein kinase) and the proline-rich tyrosine kinase 2 (Pyk2), and they can also cause robust activation of quiescent CFTR channels. In excised patch-clamp experiments, CFTR activity during exposure to Src or Pyk2 reached ∼80% of that stimulated by PKA. Exposure to PKA after Src or Pyk2 caused a further increase to the level induced by PKA alone, implying a common limiting step. Channels became spontaneously active when v-Src or the catalytic domain of Pyk2 was coexpressed with CFTR and were further stimulated by the tyrosine phosphatase inhibitor dephostatin. Exogenous Src also activated 15SA-CFTR, a variant that lacks 15 potential PKA sites and has little response to PKA. PKA-independent activation by tyrosine phosphorylation has implications for the mechanism of regulation by the R domain and for the physiologic functions of CFTR.
Parallelized Light-sheet Microscopy with Flexible and Encoded Illumination (2021)

Light Sheet Microscopy (LSM), being capable of optical sectioning at diffraction-limited resolution and at low light doses [1] , has become the tool of choice for volumetric imaging of large samples. Unfortunately, traditional LSM architectures are limited in speed because a z-stack is collected by either sample translation or synchronized movement of objective lens and light-sheet. A promising solution to avoid slow mechanical movements is extending the Depth-of-Field (DoF) of the microscope [2] , [3] and moving only the light-sheet. However, the DoF extension comes at the cost of a loss of photons, compromising the signal-to-noise ratio of the images. Here, we propose an innovative technique devoted to restoring the signal content of the images, while preserving the speed of extended DoF microscopes.
ML327 Blocks N-MYC Expression and Tumor Formation in MYCN-Amplified Neuroblastomas (2016)

Rellinger, Eric J. MD; Padmanabhan, Chandrasekhar MD; Craig, Brian T. MD; An, Hanbing PhD; Qiao, Jingbo PhD; Waterson, Alex G. PhD; Lindsley, Craig W. PhD; Beauchamp, Daniel R. MD, FACS; Chung, Dai H. MD, FACS Author Information
Spatiotemporal decomposition methods for nanobubble contrast-enhanced ultrasound (2022)

Nanobubble ultrasound contrast agents (NBs) offer enhanced access to deep tumor tissue by extrapolation from vasculature. When combined with targeting moieties, shell-stabilized nanobubbles can outperform other agents used in molecular ultrasound imaging due to their small size. The visualization and decoupling of extravasated and intravascular NBs is critical to furthering nanobubble molecular imaging with ultrasound. Spatiotemporal processing of echo data, usually via singular value decomposition (SVD), enables enhanced decoupling of signals of stationary from moving scatterers and therefore provides a novel tool for analysis of NB extravasation into the parenchyma. Instead of trivial solutions, we have developed non-negative SVD (nnSVD) methods applicable to most commercial scanners without requiring the raw data. Additionally, our formulation allows addition of proper regularizers, such as sparsity, to further expand the decomposition dimensions. We validate these methods in phantom models and present how the suggested decompositions can distinctly decouple flowing from extravasated NBs in in vivo tumour models with enhanced permeability. Our results show the successful tracking of nanobubble accumulation in tumour tissue and can serve as a relative metric for molecular targeting of prostate cancer. Further exploration of these methods could be used to improve long-term imaging and drug delivery capabilities of NBs.
Statisticum (2017)

We introduce a new concept of leveraging traditional data statistics as dynamic data integrity constraints. These data statistics produce transient database constraints, which are valid as long as they can be proven to be consistent with the current data. We denote this type of data statistics by constraint data statistics , their properties needed for consistency checking by consistency metadata , and their implied integrity constraints by implied data statistics constraints ( implied constraints for short). Implied constraints are valid integrity constraints which are powerful query optimization tools employed, just as traditional database constraints, in semantic query transformation (aka query reformulation), partition pruning, runtime optimization, and semi-join reduction, to name a few. To our knowledge, this is the first work introducing this novel and powerful concept of deriving implied integrity constraints from data statistics. We discuss theoretical aspects of the constraint data statistics concept and their integration into query processing. We present the current architecture of data statistics management in SAP HANA and detail how constraint data statistics are designed and integrated into this architecture. As an instantiation of this framework, we consider dynamic partition pruning for data aging scenarios. We discuss our current implementation for constraint data statistics objects in SAP HANA which can be used for dynamic partition pruning. We enumerate their properties and show how consistency checking for implied integrity constraints is supported in the data statistics architecture. Our experimental evaluations on the TPC-H benchmark and a real customer application confirm the effectiveness of the implied integrity constraints; (1) for 59% of TPC-H queries, constraint data statistics utilization results in pruning cold partitions and reducing memory consumption, and (2) we observe up to 3 orders of magnitude speed-up in query processing time, for a real customer running an S/4HANA application.
Curious snakes: an active contour formulation of information-driven minimum-latency boundary detection (2010)

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Detection of Listeria monocytogenes in surface swabs using a non-radioactive polymerase chain reaction-coupled ligase chain reaction assay (1995)

A non-radioactive polymerase chain reaction (PCR)-coupled ligase chain reaction (LCR) assay for the specific detection of Listeria monocytogenes was applied to swab samples from metal surfaces that were artificially inoculated with L. monocytogenes. Using a 24 h enrichment this detection system was able to consistently detect 20 cfu L. monocytogenes from a 25 cm2 metal surface, also in the presence of 2 × 105 cfu of Escherichia coli. Detection of non-viable cells resulting from treatment of the inoculated surface with a chlorinating sanitizer was eliminated by the use of a 24 h enrichment step in Listeria enrichment broth.
Costimulation Light: Activation of CD4+ T Cells with CD80 or CD86 Rather Than Anti-CD28 Leads to a Th2 Cytokine Profile (2000)

To examine the role of CD28 and CTLA-4 in Th cell differentiation, we used a novel microsphere-based system to compare the effects of CD28 ligation by Ab or CD80/CD86. One set of beads was prepared by coating with anti-CD3 and anti-CD28 Ab. Another set of beads was prepared by immobilizing anti-CD3 and murine CD80-Ig fusion protein or murine CD86-Ig fusion protein on the beads. The three sets of beads were compared in their effects on the ability to activate and differentiate splenic CD4 T cells. When purified naive CD4(+) cells were stimulated in vitro, robust proliferation of similar magnitude was induced by all three sets of beads. When cytokine secretion was examined, all bead preparations induced an equivalent accumulation of IL-2. In contrast, there was a marked difference in the cytokine secretion pattern of the Th2 cytokines IL-4, IL-10, and IL-13. The B7-Ig-stimulated cultures had high concentrations of Th2 cytokines, whereas there were low or undetectable concentrations in the anti-CD28-stimulated cultures. Addition of anti-CTLA-4 Fab augmented B7-mediated IL-4 secretion. These studies demonstrate that B7 is a critical and potent stimulator of Th2 differentiation, and that anti-CD28 prevents this effect.
Measurement of Neutralizing Antibody Responses to Influenza H5N1 (2014)

Manuscript published as part of the Options for the Control of Influenza VI meeting in Toronto, 17-23rd June 2007.
Pilot study of temporary controllable gastric pseudobezoars for dynamic non-invasive gastric volume reduction (2009)

Invasive surgical procedures for gastric volume reduction or bypass have been considered the most effective approach to sustainable long-term weight reduction. However, non-invasive techniques for dynamic volume reduction from inside the stomach are lacking. The aim of this study was to propose temporary, permeable, controllable pseudobezoars for non-invasive, long-term sustainable gastric volume reduction and to test them in pilot human studies. Permeable sac-like carriers made from biocompatible and biodegradable material were filled with expandable superabsorbent fiber and polymer granules. The implements were designed to prevent the expulsion of the pseudobezoars through the pylorus for a controlled time period. The pseudobezoars were administered transorally to two human patients (2M, 78.9 kg/174 cm, girth 88.1 cm, and 89.7 kg/175, girth 95.2 cm). Body weight dynamics, girth, level of satiety, stools, bowel regularity and notable side effects were monitored in three distinct 1 month periods: baseline, therapy and washout. Sonographic verification of the presence of pseudobezoars in the stomachs of both subjects was performed at the end of the therapy month and was repeated at the end of the washout period to examine the clearance of the implements. During the therapy month, both individuals exhibited significant weight and girth reduction (p < 0.05), and substantially increased satiety levels. The patients retained their bowel regularity and did not report any notable side effects. The temporary pseudobezoars were clearly noticeable sonographically in both patients at the end of the therapy month and cleared after its discontinuation. Controllable temporary pseudobezoars were designed and tested in pilot studies.
Scavenging in a turbocharged gasoline engine (2012)

The phenomenon of air escaping the engine intake directly to the exhaust during valve overlap is commonly known as scavenging. This phenomenon is primarily observed at low-speed, high-load in engines with significant overlap between intake valve opening and exhaust valve closing. Evaluation on a turbocharged-gasoline engine shows increased low-speed torque when operating under scavenging conditions. This paper investigates the occurrence of scavenging and analyzes its consequences. A methodology is presented to infer the amount of scavenging using airflow and in-cylinder pressure measurements. Scavenging increases catalyst exotherm when operating with stoichiometric exhaust. A model is proposed to predict the additional exotherm.
Low-noise photorefractive amplification and detection of very weak signal beams (1995)

We present theoretical and experimental analyses of the signal-to-noise ratio (SNR) of photorefractive two-wave mixing detection that uses BaTiO(3). The influence of beam fanning is taken into account in the detection process. Different known methods to enhance the SNR of the detection are theoretically and experimentally compared. A 10-fold improvement of the SNR is obtained, and the detection of a 1-pW signal intensity for a SNR of 50 is achieved for two of them.
T CELL DEPLETION OF HUMAN BONE MARROW USING MONOCLONAL ANTIBODY AND COMPLEMENT-MEDIATED LYSIS (1983)

Human bone marrow was harvested from surgically resected bones of 25 patients and was tested for the presence of mature T cells. An average of 6.5% (+/- 1.2% SE) of nucleated bone marrow cells formed spontaneous rosettes with sheep red blood cells. Functional T cells in bone marrow were also identified by characteristic responses to alloantigens and the T cell mitogens concanavalin A (Con A) and phytohemagglutinin (PHA). The ability of three monoclonal antibodies (OKT.3, Lyt-3, and (Leu-1) to lyse peripheral T cells in the presence of rabbit complement was examined. All three reagents were found to be specifically lytic for mature T cells in peripheral blood. One reagent (Leu-1) was selected for use in depletion of T cells in human bone marrow. Seven of 10 experiments performed showed sufficient T cell responses to be evaluable. In all of these experiments, a marked reduction of T cells and T cell functions was observed. On the average, E rosettes were reduced 89.2% (+/- 3.0% SE) below medium controls while the mean PHA, Con A, and mixed lymphocyte culture (MLC) activity were completely eliminated to levels below background. In four experiments, colony-forming units (CFU-GM) in bone marrow were assayed following treatment with Leu-1 and showed a mean increase of 194% (+/- 32% SE) over medium controls. Since mature T cells are thought to be responsible for graft-versus-host disease in allogeneic bone marrow transplantation, this method of T cell depletion may be useful for preparing marrow for human bone marrow transplants.