gebhart/patrepeval huggingface dataset:
Sediments underlying the Peruvian OMZ - sink or source for reactive N species (2010)

Oxygen minimum zones (OMZs) represent key regions for nitrogen (N) turnover in the water column as well as in the sediments. However, the redox dependent source-sink function of sediments for reactive nitrogen (NO3- + NO2- + NH4+) is not well established. To address this issue, we studied benthic nitrogen cycling under different bottom water oxygen concentrations along a transect traversing the Peruvian OMZ at 11°S. In situ fluxes of nitrogen species across the sediment-water interface were measured using benthic landers and the sediment geochemistry was analyzed in recovered multi-core samples. The fieldwork was conducted through (80 - 400 m water depth) and beyond (700 - 1000 m water depth) the extension of the OMZ. The relative importance of different processes in the benthic nitrogen cycle was investigated using a 1D reaction-transport model tuned to the measured data. The reaction network included the release of ammonium during organic matter mineralization, nitrification and heterotrophic denitrification, as well as anammox. Nitrite was explicitly included in the model as an independent variable. Dissimilatory nitrate reduction to ammonium (DNRA) was also considered where mats of large sulfur bacteria were observed during towed camera deployments (~ 80 - 300 m depth). The model was able to simulate the following features of the benthic N cycle determined from the in situ lander deployments: (i) at the upper fringe of the OMZ (~ 80 - 250 m), the sediments acted as a source of reactive nitrogen due to enhanced ammonium release, (ii) at the lower fringe of the OMZ (300 - 400 m), there was a net uptake of reactive nitrogen of up to ~ 1.9 mmol N m-2 d-1 , and (iii) below the OMZ, reactive nitrogen fluxes into the sediments were low (≤ 0.5 mmol N m-2 d-1 ). The model further predicted that denitrification was the major control on N2 production along the entire transect whereas anammox played a minor role (≤ 10%). At the upper fringe of the OMZ, DNRA was driving ammonium release and determined whether the sediments were a net source or sink for reactive nitrogen species. In contrast, at the lower fringe of the OMZ organic carbon mineralization was the dominant process releasing ammonium. The relative importance of DNRA versus organic carbon mineralization for ammonium release varied systematically between these two end-members along the studied transect.
Preparation of Xylan-g-/P(AA-co-AM)/GO Nanocomposite Hydrogel and its Adsorption for Heavy Metal Ions (2019)

Xylan-<i>g</i>-/P(AA-<i>co</i>-AM)/Graphene oxide (GO) hydrogels were prepared and used in the removal of heavy mental ions. Acrylamide (AM), acrylic acid (AA), and xylan were used as the raw materials to prepare the hydrogels with ammonium persulfate (APS) as the initiator. The prepared hydrogels were characterized by Fourier transform infrared (FTIR), thermogravimetric analysis (TGA), and energy dispersive X-ray (EDX). Some important properties of nanocomposite hydrogels such as swelling behavior, mechanical property, and adsorption capacity were also examined as well as the regeneration of the hydrogels. The results showed that the prepared hydrogels reached the equilibrium state of swelling after 12 h, and the compressive strength of the hydrogel with 30 mg of GO could reach up to 203 kPa. Compared with traditional hydrogel, the mechanical properties of the hydrogels with GO were obviously improved. The maximum adsorption capacity of hydrogels for Pb<sup>2+</sup>, Cd<sup>2+</sup>, and Zn<sup>2+</sup> could reach up to 683 mg/g, 281 mg/g, and 135 mg/g, respectively. After five cycles of adsorption and desorption, the recovery rate of the hydrogels on Pb<sup>2+</sup>, Cd<sup>2+</sup>, and Zn<sup>2+</sup> was still up to 87%, 80%, and 80%, respectively-all above 80%.
Electron Hopping in π-Stacked Covalent and Self-Assembled Perylene Diimides Observed by ENDOR Spectroscopy (2006)

We have carried out room-temperature, solution-phase electron paramagnetic resonance and electron-nuclear double resonance studies on a series of radical anions based upon perylene-3,4:9,10-bis(dicarboximide) (PDI). The following systems were studied: two PDI monomers, a covalent, cofacial dimer, and two covalent trefoil-PDI3 molecules, one of which self-assembles into pi-stacked dimers. Full sharing of the unpaired electron in the covalent and self-assembled dimers is revealed by a halving of the hyperfine coupling constants in these species, relative to those of the monomers. These results and the electronic absorption spectra show that electron hopping on a >107 Hz time scale occurs between a reduced and neutral chromophoric pair.
<i>Review</i> : Therapeutic Drug Monitoring of Antiretroviral Therapy (2004)

The concept of managing pharmacotherapy based on plasma drug concentrations has been used for decades in a variety of clinical settings. The interest in therapeutic drug monitoring (TDM) of antiretroviral drugs has grown significantly since highly active antiretroviral therapy (HAART) became a standard of care in clinical practice. A primary characteristic of TDM of antiretroviral drugs is that multiple agents are concomitantly used in HAART regimens. Inadequate drug concentrations may lead to evolution of drug resistance mutations and endanger present and future treatment options. A number of clinical trials have demonstrated that drug serum concentrations are an important factor in response to therapy for HIV, but whether TDM will become a tool for the routine management of HIV infection remains to be determined. This review includes an illustrative case report of measuring concentrations of antiretroviral drugs in a pediatric patient.
From artifacts to aggregations: Modeling scientific life cycles on the semantic Web (2009)

Abstract In the process of scientific research, many information objects are generated, all of which may remain valuable indefinitely. However, artifacts such as instrument data and associated calibration information may have little value in isolation; their meaning is derived from their relationships to each other. Individual artifacts are best represented as components of a life cycle that is specific to a scientific research domain or project. Current cataloging practices do not describe objects at a sufficient level of granularity nor do they offer the globally persistent identifiers necessary to discover and manage scholarly products with World Wide Web standards. The Open Archives Initiative's Object Reuse and Exchange data model (OAI‐ORE) meets these requirements. We demonstrate a conceptual implementation of OAI‐ORE to represent the scientific life cycles of embedded networked sensor applications in seismology and environmental sciences. By establishing relationships between publications, data, and contextual research information, we illustrate how to obtain a richer and more realistic view of scientific practices. That view can facilitate new forms of scientific research and learning. Our analysis is framed by studies of scientific practices in a large, multidisciplinary, multi‐university science and engineering research center, the Center for Embedded Networked Sensing.
Molecular cytogenetics localizes two new breakpoints on 11q23.3 and 21q11.2 in myelodysplastic syndrome with t(11;21) translocation (1999)

Translocation t(11;21)(q24;q11.2) is a rare but recurrent chromosomal abnormality associated with myelodysplastic syndrome (MDS) that until now has not been characterized at the molecular level. We report here results of a molecular cytogenetic analysis of this translocation in a patient with refractory anemia. Using FISH with a panel of 11q and 21q cosmid/YAC probes, we localized the chromosome 11 breakpoint at q23.3 in a region flanked by CP-921G9 and CP-939H3 YACs, distal to the HRX/MLL locus frequently involved in acute leukemias. The chromosome 21 breakpoint was mapped in a 800-kb fragment inserted into the CP-145E3 YAC at 21q11.2, proximal to the AML1 gene. It is noteworthy that in all four cases with a t(11;21) reported until now, a second der(11)t(11;21) and loss of normal chromosome 11 could be observed either at diagnosis or during the course of the disease. Since in our case heteromorphism was detected by FISH on the centromeric region of the two der(11), the second der(11) chromosome could be the result of a mitotic recombination that had occurred on the long arm of chromosome 11, rather than of duplication of the original der(11). Constancy of secondary karyotypic changes resulting in an extra copy of the putative chimeric gene at der(11), loss of 11 qter sequences, and partial trisomy 21 suggest that neoplastic progression of MDS cases with a t(11;21) may be driven by the same mechanism(s).
Performance of a TthPrimPol-based whole genome amplification kit for copy number alteration detection using massively parallel sequencing (2016)

Starting from only a few cells, current whole genome amplification (WGA) methods provide enough DNA to perform massively parallel sequencing (MPS). Unfortunately, all current WGA methods introduce representation bias which limits detection of copy number aberrations (CNAs) smaller than 3 Mb. A recent WGA method, called TruePrime single cell WGA, uses a recently discovered DNA primase, TthPrimPol, instead of artificial primers to initiate DNA amplification. This method could lead to a lower representation bias, and consequently to a better detection of CNAs. The enzyme requires no complementarity and thus should generate random primers, equally distributed across the genome. The performance of TruePrime WGA was assessed for aneuploidy screening and CNA analysis after MPS, starting from 1, 3 or 5 cells. Although the method looks promising, the single cell TruePrime WGA kit v1 is not suited for high resolution CNA detection after MPS because too much representation bias is introduced.
Three new allelic mouse mutations that cause skeletal overgrowth involve the natriuretic peptide receptor C gene ( <i>Npr3</i> ) (1999)

In 1979, a BALB/cJ mouse was identified with an exceptionally long body. This phenotype was found to be caused by a recessive mutation, designated longjohn (lgj), that mapped to the proximal region of chromosome 15. Several years later, a mouse with a similarly elongated body was identified in an outbred stock after chemical mutagenesis with ethylnitrosourea. This phenotype also was caused by a recessive mutation, designated strigosus (stri). The two mutations were found to be allelic. A third allele was identified in a DBA/2J mouse and was designated longjohn-2J (lgj(2J)). Analysis of skeletal preparations of stri/stri mice indicated that the endochondral ossification process was slightly delayed, resulting in an extended proliferation zone. A recent study reported that mice overexpressing brain natriuretic peptide, one of the members of the natriuretic peptide family, exhibit a skeletal-overgrowth syndrome with endochondral ossification defects. The Npr3 gene coding for type C receptor for natriuretic peptides (NPR-C), which is mainly involved in the clearance of the natriuretic peptides, mapped in the vicinity of our mouse mutations and thus was a candidate gene. The present study reports that all three mutations involve the Npr3 gene and provides evidence in vivo that there is a natriuretic-related bone pathway, underscoring the importance of natriuretic peptide clearance by natriuretic peptide type C receptor.
Clinical trials of bisphosphonates in multiple myeloma. (2012)

More than 80% of patients with multiple myeloma (MM) have osteolytic bone disease, which increases the risk of skeletal-related events (SREs) such as pathologic fracture, spinal cord compression, and the need for radiotherapy or surgery. Bone disease is primarily due to increased osteoclastic activity and impaired osteoblast activity. Bisphosphonates are pyrophosphate analogues with high bone affinity that can inhibit osteoclastic activity. Pamidronate and zoledronic acid are the most commonly used bisphosphonates in multiple myeloma. Other agents include ibandronate and clodronate. Bisphosphonates are associated with several adverse events, such as renal toxicity and osteonecrosis of the jaw. The optimal duration of bisphosphonate therapy has yet to be determined. Clinical trials are investigating tailored approaches to management based on treatment-related changes in levels of bone resorption markers.
Serum levels of pregnancy associated alpha 2-glycoprotein (alpha 2-PAG) during pregnancy in autoimmune thyroid disease: relationship to disease activity. (1985)

Serum concentrations of pregnancy associated alpha 2-glycoprotein (alpha 2-PAG) were measured serially by an enzyme linked immunosorbent assay during 24 pregnancies in 18 patients with Graves' disease and four with Hashimoto's thyroiditis. During each trimester, alpha 2-PAG levels were significantly higher than in normal pregnant controls, matched for week of gestation. Patients showing remission of disease activity had progressively higher alpha 2-PAG levels throughout pregnancy than those with active disease. The data support the idea that alpha 2-PAG may play an important role in inducing and maintaining the clinical remissions observed in some women with autoimmune thyroid disease during pregnancy.
PENETRATION OFWINDELECTRIC CONVERSION SYSTEMS INTOTHEUTILITY GRID (1985)

Thispaperisconcerned withthedevelopment of appropriate modelsfortheinterconnected operation ofwindgenerator clusters withanautonomous power systemandsimulation techniques forthestudyof thedegree of penetration ofsuchwindelectric conversion devices whenoperating inparallel with theutility grid.Thequality oftheinterconnected systemperformance isspecified intermsofoperationalconstraints and theresultant penetration strategyis implemented viaa microprocessor-based control scheme.Thestrategy assuresasatisfactory levelofsystemperformance whileoptimizing the available energytransfer fromthewindgenerators totheutility grid.
Exchange bias system of Fe/KFeF3 (2004)

Epitaxial Fe/KFeF3 bilayers were grown using molecular beam epitaxy on GaAs (100). FMR measurements revealed two peaks for samples with an Fe seed layer. A peak with fourfold symmetry was identified as the main layer Fe whereas a peak with twofold symmetry appeared to be due to the seed layer Fe. The magnetocrystalline anisotropy for the fourfold peak is ∼400 Oe at 300 K whereas a large anisotropy of 1.5 kOe is associated with the seed layer. A large rotatable anisotropy of 280±20 Oe was found for a sample with Fe thickness 2.1 nm. All Fe/KFeF3 bilayers checked by superconducting quantum interference device exhibit exchange bias and enhanced coercivity. The blocking temperature of the system is close to the Néel temperature 112 K of KFeF3. One sample has polycrystalline KFeF3 and shows a much larger exchange bias and coercivity than the samples having single crystal KFeF3.
<i>Scanning Electron Microscopy</i> (1975)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation O. C. Wells, L. L. Marton; Scanning Electron Microscopy. Physics Today 1 July 1975; 28 (7): 52. https://doi.org/10.1063/1.3069062 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
P1155REMOVAL OF PHOSPHATE AND CREATININE DURING PD WITH DIFFERENT GLUCOSE CONCENTRATIONS (2020)

Abstract Background and Aims Adequate removal of creatinine and phosphate is one of the key objectives in peritoneal dialysis (PD). Whereas the mechanism of creatinine removal is well known, there are gaps in understanding regulation of phosphate removal. Clinical studies show that although the size of both molecules is similar, their removal might behave differently (Badve et al CJASN 2008). Several, but not all, studies have suggested that peritoneal phosphate clearance is larger when using CAPD than APD prescriptions, suggesting the dwell time or duration is an important determinant of phosphate clearance. The aim of the study was to investigate specifically the effect of dwell duration at the level of single PD exchange with different glucose concentrations on peritoneal phosphate clearance. Method A prolonged 8-hour PET was carried out in 32 clinically stable PD patients with each of three glucose-based solutions: 1.36% (G1), 2.27% (G2), and 3.86% (G3) with temporary drainage at 1 and 4 hours of peritoneal dwell. Dialysate and blood samples were taken to measure infused and drained volume and concentration of phosphate and creatinine in dialysate and blood. Clearances were calculated for a single exchange for each solution and for 4-hour (4H) and 8-hour (8H) dwell periods. For each patient, the 4-hour creatinine D/P ratio for G3 was calculated. The clearance ratio, ClR, defined as the ratio of solute clearance for particular solution to its clearance for the G1 solution, was calculated for both solutes and each solution and dwell durations. Results The obtained values of 4H creatinine D/P ratio for G3 solution were 0.67±0.11 (mean±SD). The values of solute clearances per single exchange expressed in mL/min, are presented in table below. Creatinine and phosphate clearances were found to be solution and dwell duration dependent with p&amp;lt;0.001. The clearances of both solutes were correlated for the same dwell duration or solution (not for creatinine G2 for 4H vs 8H) with p&amp;lt;0.05. Moreover, solute clearances were also correlated with creatinine D/P for 4H but not for 8H. The clearances of phosphate were also correlated with that for creatinine each solution at both dwell durations with p&amp;lt;0.001. Both calculated ClR were found to be dependent on the solution (p&amp;lt;0.001) but not dwell duration. Similar dependence on solution and correlations are valid in one analyze solute mass removal. Conclusion Phosphate and creatinine clearances were found to be well correlated during a long, 8-hour PET proving similarities in their transport. Interestingly, the dependence of both clearances and ClR on solution glucose concentration suggest that the removal of phosphate as well as creatinine depends on the ultrafiltration induced by glucose concentration in dialysis solution.
ChemInform Abstract: A Convenient Terminal Allene Synthesis from Propargylic Acetates. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it (2013)

Despite the sequencing of the human genome, the rate of innovative and successful drug discovery in the pharmaceutical industry has continued to decrease. Leaving aside regulatory matters, the fundamental and interlinked intellectual issues proposed to be largely responsible for this are: (a) the move from 'function-first' to 'target-first' methods of screening and drug discovery; (b) the belief that successful drugs should and do interact solely with single, individual targets, despite natural evolution's selection for biochemical networks that are robust to individual parameter changes; (c) an over-reliance on the rule-of-5 to constrain biophysical and chemical properties of drug libraries; (d) the general abandoning of natural products that do not obey the rule-of-5; (e) an incorrect belief that drugs diffuse passively into (and presumably out of) cells across the bilayers portions of membranes, according to their lipophilicity; (f) a widespread failure to recognize the overwhelmingly important role of proteinaceous transporters, as well as their expression profiles, in determining drug distribution in and between different tissues and individual patients; and (g) the general failure to use engineering principles to model biology in parallel with performing 'wet' experiments, such that 'what if?' experiments can be performed in silico to assess the likely success of any strategy. These facts/ideas are illustrated with a reasonably extensive literature review. Success in turning round drug discovery consequently requires: (a) decent systems biology models of human biochemical networks; (b) the use of these (iteratively with experiments) to model how drugs need to interact with multiple targets to have substantive effects on the phenotype; (c) the adoption of polypharmacology and/or cocktails of drugs as a desirable goal in itself; (d) the incorporation of drug transporters into systems biology models, en route to full and multiscale systems biology models that incorporate drug absorption, distribution, metabolism and excretion; (e) a return to 'function-first' or phenotypic screening; and (f) novel methods for inferring modes of action by measuring the properties on system variables at all levels of the 'omes. Such a strategy offers the opportunity of achieving a state where we can hope to predict biological processes and the effect of pharmaceutical agents upon them. Consequently, this should both lower attrition rates and raise the rates of discovery of effective drugs substantially.
Selective preconcentration and online collection of charged molecules using ion concentration polarization (2015)

Online collection of selectivity preconcentrated analytes was demonstrated utilizing ion concentration polarization phenomena and pneumatic valve system.
Protease-Catalyzed Peptide Synthesis on Solid Support (2002)

The direct enzymatic synthesis of peptides from amino acids is widely used as a useful alternative to chemical synthesis. However, good yields of such enzyme-catalyzed reactions require altered reaction conditions to overcome the bias for hydrolysis in aqueous medium. We argue that the synthesis/hydrolysis equilibrium can be shifted toward synthesis in aqueous medium by immobilizing the amine on solid support. In this report, we show the first examples of solid-phase peptide synthesis catalyzed by a protease in bulk aqueous buffer.
WaveScheduling (2004)

Sensor networks are being increasingly deployed for diverse monitoring applications. Event data are collected at various sensors and sent to selected storage nodes for further in-network processing. Since sensor nodes have strong constraints on their energy usage, this data transfer needs to be energy-efficient to maximize network lifetime. In this paper, we propose a novel methodology for trading energy versus latency in sensor database systems. We propose a new protocol that carefully schedules message transmissions so as to avoid collisions at the MAC layer. Since all nodes adhere to the schedule, their radios can be off most of the time and they only wake up during well-defined time intervals. We show how routing protocols can be optimized to interact symbiotically with the scheduling decisions, resulting in significant energy savings at the cost of higher latency. We demonstrate the effectiveness of our approach by means of a thorough simulation study.
The future of recombinant host defense peptides (2022)

The antimicrobial resistance crisis calls for the discovery and production of new antimicrobials. Host defense peptides (HDPs) are small proteins with potent antibacterial and immunomodulatory activities that are attractive for translational applications, with several already under clinical trials. Traditionally, antimicrobial peptides have been produced by chemical synthesis, which is expensive and requires the use of toxic reagents, hindering the large-scale development of HDPs. Alternatively, HDPs can be produced recombinantly to overcome these limitations. Their antimicrobial nature, however, can make them toxic to the hosts of recombinant production. In this review we explore the different strategies that are used to fine-tune their activities, bioengineer them, and optimize the recombinant production of HDPs in various cell factories.