gebhart/patrepeval huggingface dataset:
Molecular insights into the inhibition of plasmepsins by HIV-1 protease inhibitors: Implications for antimalarial drug discovery (2021)

1. Abstract Malaria is a deadly disease, and the worldwide emergence of drug resistance in the Plasmodium parasites demands the development of novel and potent antimalarials. HIV-1 protease inhibitors (HIV-1 PIs) alleviate the Plasmodium pathogenesis during malaria/HIV-1 co-infection plausibly by inhibiting vacuolar plasmepsins (PMs), the hemoglobin degrading proteases from P. falciparum . All five FDA-approved HIV-1 PIs tested against PMII exhibit the K i values in the low micromolar range of which RTV and LPV display the highest inhibition activity. Both inhibitors impede in vitro growth of P. falciparum at low micromolar IC 50 values. We report the first crystal structures of PMII complexed with RTV and LPV that reveal the binding mode and interactions of the inhibitors in the active site as well as elucidate the mechanism underlying their differential potency. The conformational flexibility of the P4 group in RTV allows it to explore multiple regions of the S4 pocket. The present study establishes vacuolar PMs as potential drug targets of HIV-1 PIs. The molecular details explaining the inhibitory mechanism of HIV-1 PIs might be crucial in designing novel and potent antimalarial analogs. This work strengthens the prospect of drug repurposing as an alternative strategy towards antimalarial treatments and provides an opportunity to tackle malaria and HIV-1 co-infection.
Compensatory enlargement of Ossabaw miniature swine coronary arteries in diffuse atherosclerosis (2015)

Studies in human and non-human primates have confirmed the compensatory enlargement or positive remodeling (Glagov phenomenon) of coronary vessels in the presence of focal stenosis. To our knowledge, this is the first study to document arterial enlargement in a metabolic syndrome animal model with diffuse coronary artery disease (DCAD) in the absence of severe focal stenosis. Two different groups of Ossabaw miniature pigs were fed a high fat atherogenic diet for 4 months (Group I) and 12 months (Group II), respectively. Group I (6 pigs) underwent contrast enhanced computed tomographic angiography (CCTA) and intravascular ultrasound (IVUS) at baseline and after 4 months of high fat diet, whereas Group II (7 pigs) underwent only IVUS at 12 months of high fat diet. IVUS measurements of the left anterior descending (LAD), left circumflex (LCX) and right coronary (RCA) arteries in Group I showed an average increase in their lumen cross-sectional areas (CSA) of 25.8%, 11.4%, and 43.4%, respectively, as compared to baseline. The lumen CSA values of LAD in Group II were found to be between the baseline and 4 month values in Group I. IVUS and CCTA measurements showed a similar trend and positive correlation. Fractional flow reserve (FFR) was 0.91 ± 0.07 at baseline and 0.93 ± 0.05 at 4 months with only 2.2%, 1.6% and 1% stenosis in the LAD, LCX and RCA, respectively. The relation between percent stenosis and lumen CSA shows a classical Glagov phenomenon in this animal model of DCAD.
Laser scribe silver-reduced graphene oxide as novel bactericidal filter (2019)

A novel method for the synthesis of reduced graphene Oxide silver (rGOAg) nanocomposite has been developed for the antibacterial performance. Graphene Oxide (GO) was used as a supporting material towards formation of silver nanoparticle (AgNPs) by a simple microwave irradiation on mixture of GO and silver complexes. The obtained nanocomposite were characterized by using Ultraviolet-visible spectroscopy (UV-Vis), Xray diffraction (XRD) to confirm the formation of rGOAg. The surface morphological studies for the nanocomposite was done by using high resolution transmission electron microscope (HRTEM). Nanometer-sized AgNPs (an average diameter of about 17 nm) with spherical-shape structure loaded on the rGO layer showed a good antibacterial towards Methicillin-resistant Staphylococcus aureus (MRSA).
Dynamically Accessing Packet Header Fields at High-Speed (2011)

A significant part of packet processing consists of detecting whether certain standard protocol headers are present, where they are located and whether they include optional information. Packet processing programs are on tight time budgets, especially to handle speeds in the gigabits per second (gbps) range. Thus, high-speed mechanisms for finding and accessing headers are critical. Our approach lets users define headers as C-style structures in a high-level language, packetC [1], and specify header locations in terms of offsets from the start of the current packet, which is treated as an array of unsigned bytes. These offsets can be expressed in terms of network layer offsets, constant values, runtime-calculated variables and combinations of all of these. This paper focuses on the principal forms these offset expressions can take and on how our FPGAs (Field Programmable Gate Arrays), compiler and interpreter collectively handle them at runtime. For simple and complex header offset scenarios we provide users with intuitive, high-level ways to describe offsets and provide effective runtime mechanisms to access header fields.
Yb-doped Bismuthate Glass waveguide laser fabricated by Ultrafast Laser Inscription (2012)

We demonstrate laser action from an ultrafast laser inscribed Yb doped bismuthate glass waveguide. When pumped using a 975 nm diode laser, efficient lasing was observed at 1059 nm with a maximum output power of 148 mW and a slope efficiency of 64%.
Calcium-sensing receptor expression and regulation by extracellular calcium in the AtT-20 pituitary cell line. (1996)

A 120 kDa, G protein-coupled calcium-sensing receptor (CaR) was recently identified and cloned from bovine parathyroid and rat kidney. We report here that a similar calcium-sensing receptor is also present in rat and mouse pituitary as well as in the mouse pituitary cell line, AtT-20. Fragments (383-bp) of the extracellular domain of the calcium-sensing receptor from the AtT-20 cells and mouse pituitary were amplified by RT-PCR, sequenced, and found to be identical. By Northern blot analysis, AtT-20 cells expressed a major CaR mRNA transcript of 7.5 kb and three minor transcripts of 9.5, 4.0, and 1.5 kb. Except for the 9.5-kb species, these CaR transcripts were also found to be present in mouse kidney, where the 7.5-kb transcript was again the predominant form. The presence of the CaR protein in AtT-20 cells was documented directly by fluorescence immunocytochemistry using an antibody directed against the extracellular domain of the CaR. Exposure of AtT-20 cells to increasing extracellular calcium concentrations from 0.3 t 3 mM for 24 h resulted in a 2- to 4-fold increase in the levels of CaR mRNA, but not of the RNAs for beta-actin or POMC. The CaR appeared to be functional in AtT-20 cells, since acute increases in extracellular calcium between 2 and 5 mM induced increases in the cellular content of total inositol phosphates, cytosolic calcium, and cAMP. This report suggests that pituitary cells respond to changes in extracellular calcium via a G protein-coupled CaR.
Coiled Tubing as Initial Production Tubing: An Overview of Case Histories (1995)

Summary From Jan. 1993 through Feb. 1995 Marathon Oil Co. completed 23 newly drilled gas wells with coiled tubing as the initial production string. This paper reviews operational aspects of representative jobs, summarizes areas where improvements in equipment and technique were implemented, and addresses cost and productivity benefits of rigless completions. A summary of lessons learned is also included. Introduction Marathon has used coiled tubing for initial production tubing in several wells to match the tubing to the well productivity, to unload fracture fluids as quickly as possible, and to minimize cost by reducing the time the drilling rig stays on location. Use of coiled tubing allows tubing size to be matched closely to the performance of relatively low rate wells, minimizing the tubular costs and improving the well's ability to stay unloaded. In areas with water-sensitive formations, live-well completion prevents formation damage associated with kill fluids. The main areas of improvement from one job to the next involved the use of a pressurized, hydraulically operated access window, ensuring that all fracture sand was cleaned out before landing the coiled tubing and using a "hot-cutoff' system to make the final cut on the coil tubing. An additional benefit is that no fluid is lost to the formation during the completion. Lessons learned include keeping the coiled-tubing size large enough to run smaller coiled tubing through it for cleanout and slickline work, care in closing blowout preventer (BOP) rams to avoid damaging the coiled tubing, and the use of wellhead equipment specifically designed for use with coiled tubing. This technique is especially suited to low pressure and water-sensitive reservoirs where fluid loss is a concern. An additional benefit is the cost savings from reducing the hole and casing sizes to match the reservoir potential. In addition, this completion technique is often quicker than using a conventional completion rig and jointed tubing.
A Sensor Management Model Using Simulation-Based Approximate Dynamic Programming (2003)

This paper presents a new approach to sensor management of distributed sensor networks (DSNs). Given the current proliferation of remote sensors and their inherent resource constraints, DSN managers face a growing problem of managing the tradeoff between DSN performance and resource consumption. Our model, the Sensor Network Optimal OPerations Simulator, or SNOOPS, addresses this tradeoff by identifying a DSN control strategy that reaches an acceptably certain representation of the search region while minimizing operating costs. The core of the SNOOPS model is an approximate dynamic programming (ADP) process that uses simulation-based policy Iteration to identify an efficient DSN control strategy. Results indicate that the SNOOPS-recommended DSN control strategy improves the efficiency of DSN operations by up to 47 percent over the Base Policy of activating all sensors. In addition to determining efficient DSN control strategies, our model also provides a research base to (1) investigate the fusion of observations from disparate sensors, (2) demonstrate the use of non-imaging sensors to provide adequate situational awareness where precision emplacement of more-capable sensors is not possible, and (3) develop operational concepts to integrate DSN operations with user needs.
Palladium‐Catalyzed Direct Denitrogenative C‐3‐Arylation of 1H‐Indoles with Arylhydrazines using Air as the Oxidant (2013)

Abstract A novel palladium‐catalyzed approach to direct C‐3‐arylation of 1 H ‐indoles with arylhydrazines using air as the oxidant via CN bond cleavage has been developed. Various substituents are tolerated in this system in moderate to good yields. This reaction could also be compatible with a larger scale. Thus, this strategy using arylhydrazines as arylating reagents provides a powerful method for constructing substituted 3‐aryl‐1 H ‐indoles.
Calculating Sample Size Estimates for RNA Sequencing Data (2013)

Our results provide a needed reference for ensuring RNA-Seq gene expression studies are conducted with the optimally sample size, power, and sequencing depth. We also make available both R code and an Excel worksheet for investigators to calculate for their own experiments.
Synthesis and antibacterial activity of new quinolones containing a 7-[3-(1-amino-1-methylethyl)-1-pyrrolidinyl] moiety. Gram-positive agents with excellent oral activity and low side-effect potential (1994)

A series of the R and S isomers of 7-[3-(1-amino-1-methylethyl)-1-pyrrolidinyl]-1,4-dihydro-4-oxoquinoline- and 1,8-naphthyridine-3-carboxylic acids was prepared to determine the effect on potency of the two methyl groups adjacent to the distal nitrogen in the pyrrolidinyl moiety. The antibacterial efficacy of these dimethylated derivatives was compared to the relevant 7-[3-(aminomethyl)-1-pyrrolidinyl] parent compounds and, to a lesser extent, the 7-[3-(1-aminoethyl)-1-pyrrolidinyl] analogues. The activity of the title and reference compounds was assayed in vitro using an array of Gram-negative and Gram-positive organisms and in vivo using a mouse infection model. Selected derivatives were then screened for potential side effects in a phototoxicity mouse model and an in vitro mammalian cell cytotoxicity protocol. The results showed that the R isomer displayed a 2-20-fold advantage in activity in vitro and a 2-15-fold advantage in vivo over the S isomer. Although equipotent to the 7-[3-(aminomethyl)-1-pyrrolidinyl] parent compounds in vitro, the R isomers of the 7-[3-(1-amino-1-methylethyl)-1-pyrrolidinyl] analogues showed a dramatic increase in in vivo potency, especially via the oral route of administration. These same R isomers also appeared to possess a reduced risk of phototoxicity and cytotoxicity. This combination of superior in vivo performance with a low degree of phototoxicity and mammalian cell cytotoxicity recommends these agents for further study. Of these agents, naphthyridine 16-R represents the optimal blend of potency and safety.
Phylogenetic relationship of Plasmodium falciparum populations in the Philippines. (2008)

Malaria is one of the major infectious diseases in the Philippines. It is being targeted for control through sustained early diagnosis, treatment and mosquito control. It is in this light that understanding the genetic background of the parasite population is important not only for basic biology of the organism but also for epidemiology and control of the disease. In the present study, molecular phylogenetic relationships of the 3 Plasmodium falciparum populations in the Philippines with the other populations in the world were inferred based on polymorphisms of 9 highly polymorphic microsatellite DNA loci in the parasite genome. A total of 92 P. falciparum isolates collected from 3 provinces (Kalinga, Palawan and Davao del Norte) in the Philippines, and 8 from other populations (3 African, 2 South American, 2 Papua New Guinean, and 1 Thai) that were previously reported, were used for the analysis. The phylogenetic tree showed that the 3 Philippine populations were genetically divergent from each other as compared to the other populations. The branching pattern of the tree suggests that the 3 Philippine populations were relatively close to the Thai population, rather than the Papua New Guinean populations, indicating that the ancestor of the 3 Philippines populations were introduced from Indochina peninsula, and not from countries located south of the Philippines such as Papua New Guinea or Indonesia.
Effect of parathormone on insulin and glucagon secretion by the perfused rat pancreas (1974)

info:eu-repo/semantics/published
A novel method and device for solder joint quality inspection by using laser ultrasound (2002)

A novel, non-contact, non-destructive, on-line approach for flip chip, ball grid array (BGA), chip scale and micro BGA solder joint quality inspection is presented. In this technique, a pulsed laser generates ultrasound on the chip's surface, exciting die whole chip into a vibration motion. An interferometer was used to measure the vibration displacement of the chip's surface. Changes of solder joint quality produce different vibration responses. A signal-processing algorithm was developed to measure the difference between a good chip and chip with defects, both in time domain and frequency domain. The inspection system was characterized, and results are presented for two cases of flip chips with missing solder balls. Results indicate that this laser ultrasonic/interferometeric system offers great promise for solder bump inspection in flip chip, BGA, chip scale and micro BGA packages.
Presence of transplantable T-lymphoid cells in C57BL/6 mice infected with murine AIDS virus (1992)

The Duplan strain of murine leukemia virus induces murine AIDS in C57BL/6 mice. When spleen cells from C57BL/6 mice infected with the virus were transplanted into nude mice, subcutaneous solid tumors at the transplanted sites were formed and splenomegaly and lymphadenopathy were induced. These transplantable cells were Thy-1- CD4+ alpha-beta T-cell receptor-positive T cells and integrated with the pathogenic defective viral genome. These results indicate that neoplastic cells of T-cell lineage were induced by infecting C57BL/6 mice with murine AIDS virus.
Multiphoton fabrication of periodic structures by multibeam interference of femtosecond pulses (2003)

Femtosecond laser pulses are useful for laser microfabrication through multiphoton absorption. However, it is difficult to create interference of femtosecond pulses for the fabrication of periodic structures. In this letter, we report the fabrication of two-dimensional periodic structures by means of multibeam interference of femtosecond pulses. Scanning electron microscopy revealed a rod structure arranged into a square lattice. The possibility of controlling the period of the lattice, rod thickness, and rod shape were demonstrated.
Disorders of Neutrophil Number and Function (2006)

This review of disorders of neutrophil number and function will discuss important research advances in the field and then provide a clinical diagnostic approach. The focus will be on two recent clinical developments in the field of phagocyte disorders. First, an important natural history study from the Severe Chronic Neutropenia International Registry has recently quantitated the incidence and risk factors for death from sepsis and for progression to myelodysplastic syndrome and acute myeloid leukemia in a large cohort of severe chronic neutropenia patients, many of whom were followed 10 or more years on treatment with granulocyte colony-stimulating factor. Second, in the past year, a multinational group has announced successful gene therapy of two adults with chronic granulomatous disease, the most common disorder of neutrophil function. However, monitoring of retroviral insertion sites revealed expansion of the multiclonal population of gene-modified cells, raising concerns about eventual leukemogenesis. The review also provides a pragmatic approach to the evaluation of a patient with a suspected disorder of neutrophil number or function.
A randomized, placebo-controlled trial on the effects of soy protein containing isoflavones on quality of life in postmenopausal women (2005)

In conclusion, the findings in this randomized trial do not support the presence of a marked effect of soy protein substitution on quality of life (health status, life satisfaction, and depression) in elderly postmenopausal women.
The Effects of Thrombocytopenia on the Activated Coagulation Time (1996)

The activated coagulation (clotting) time (ACT) is widely used to monitor heparin therapy during cardiopulmonary bypass (CPB).Since thrombocytopenia occurs during and for some time after CPB, we considered the possibility that thrombocytopenia may affect the ACT. Blood samples were obtained from 12 healthy volunteers. Thrombocytopenic samples were created by a differential centrifugation technique. Blood samples from five thrombocytopenic patients were also studied. The platelet counts of the control citrated whole blood samples were 254,000 +/- 35,000/micro L (mean +/- SD), whereas the platelet counts of the thrombocytopenic citrated samples were 49,000 +/- 8000/micro L. There were no significant differences in the ACTs between these two groups (143 +/- 8 vs 145 +/- 9 s, respectively, P = 0.16). There were also no significant differences in the ACTs of the heparinized control samples compared with the ACTs of the heparinized thrombocytopenic samples. The platelet counts of the five thrombocytopenic patients were 43,000, 18,000, 16,000, 8000, and 7000/micro L, and the ACTs of the unanticoagulated samples were 162, 240, 191, 210, and 215 s, respectively. We conclude that the ACT is not affected by moderate thrombocytopenia and therefore this test may be used in patients who are moderately thrombocytopenic. (Anesth Analg 1996;83:1185-88)
Reverse Engineering of Event Handlers of RAD-Based Applications (2011)

Businesses are more and more modernising the legacy systems they developed with Rapid Application Development (RAD) environments, so that they can benefit from the new platforms and technologies. When facing the modernisation of applications developed with RAD environments, developers must deal with event handling code that typically mixes concerns such as GUI and business logic. In this paper we propose a model-based approach to tackle the reverse engineering of event handlers in RAD-based applications. Event handling code is transformed into an intermediate representation that captures the high-level behaviour of the code. From this representation, some modernisation tasks can be automated, and we propose the migration to a different architecture as an example. In particular, from PL/SQL code, a new Ajax application will be generated, where business logic, user interface and control code have been separated.
Synthesis of ortho‐Perfluoroalkyl Phenones from Hemifluorinated Enones as Key Building Blocks. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Pipe penetration inspection and repair equipment (1986)

Management of Hg-contaminated sites poses particular challenges because methylmercury (MeHg), a potent bio-accumulative neurotoxin, is formed in the environment, and concentrations are not generally predictable based solely on total Hg (THg) concentrations. In this review, we examine the state of knowledge regarding the chemical, biological, and physical controls on MeHg production and identify those most critical for contaminated site assessment and management. We provide a list of parameters to assess Hg-contaminated soils and sediments with regard to their potential to be a source of MeHg to biota and therefore a risk to humans and ecological receptors. Because some measurable geochemical parameters (e.g., DOC) can have opposing effects on Hg methylation, we recommend focusing first on factors that describe the potential for Hg bio-accumulation: site characteristics, Hg and MeHg concentrations, Hg availability, and microbial activity, where practical. At some sites, more detailed assessment of biogeochemistry may be required to develop a conceptual site model for remedial decision making. Integr Environ Assess Manag 2017;13:249-263. © 2016 SETAC.