gebhart/patrepeval huggingface dataset:
Review of chemical sensors for physiological measurement (1988)

The continuous measurement of chemical species is important for physiological and biochemical research and for critical care medicine. Chemical sensors are being developed for the measurement of a wide range of analytes, especially gases, vapours, ions, catabolites, drugs and hormones. The mechanical form of these sensors may be adapted for use in single cells, tissue fluid and blood vessels, on the skin surface, in the respiratory and gastrointestinal systems. Optical and electro-chemical principles are now used widely for sensor design, and advances in electronic fabrication methods and in optical fibres, sources, and detectors, have been important.
The Double-Edged Sword of Autophagy Modulation in Cancer (2009)

Macroautophagy (autophagy) is a lysosomal degradation pathway for the breakdown of intracellular proteins and organelles. Although constitutive autophagy is a homeostatic mechanism for intracellular recycling and metabolic regulation, autophagy is also stress responsive, in which it is important for the removal of damaged proteins and organelles. Autophagy thereby confers stress tolerance, limits damage, and sustains viability under adverse conditions. Autophagy is a tumor-suppression mechanism, yet it enables tumor cell survival in stress. Reconciling how loss of a prosurvival function can promote tumorigenesis, emerging evidence suggests that preservation of cellular fitness by autophagy may be key to tumor suppression. As autophagy is such a fundamental process, establishing how the functional status of autophagy influences tumorigenesis and treatment response is important. This is especially critical as many current cancer therapeutics activate autophagy. Therefore, efforts to understand and modulate the autophagy pathway will provide new approaches to cancer therapy and prevention.
Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components (2011)

The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation. Perhaps the most promising approach involves the application of "cellulase-enhancing factors," such as those from the glycoside hydrolase (CAZy) GH61 family. Here we show that GH61 enzymes are a unique family of copper-dependent oxidases. We demonstrate that copper is needed for GH61 maximal activity and that the formation of cellodextrin and oxidized cellodextrin products by GH61 is enhanced in the presence of small molecule redox-active cofactors such as ascorbate and gallate. By using electron paramagnetic resonance spectroscopy and single-crystal X-ray diffraction, the active site of GH61 is revealed to contain a type II copper and, uniquely, a methylated histidine in the copper's coordination sphere, thus providing an innovative paradigm in bioinorganic enzymatic catalysis.
Why You Need Smart Enough Systems (2007)

It is commonly believed that the computer-based systems most organizations rely on to support their businesses are not very smart. Many of the business decisions these companies make tend to be hidden in systems that make poor decisions, or don't make them at all. Further, most systems aren't configured to learn from the past and therefore struggle to keep up with the pace of change. While many organizations believe the answer is to implement newer, intelligent systems, the fact is that much of today's existing technology has the potential to be to make a big difference to an organization's business.This digital Short Cut lays out a cry for systems that are smart enough to help companies survive and thrive in the world as it is today. Showing how the neglect of operational decisions prevents effective implementation of strategy and describing the characteristics of effective operational decision-making, the Short Cut establishes the role of operational decisions. The characteristics of the smart enough systems modern business needs are explained, and the absolute requirement for a new approach is outlined.This Short Cut is a reproduction of the “Smart Enough Systems Manifesto” and “Why You Need Smart Enough Systems” chapters from the book.This Short Cut should be of interest to software and business professionals. In particular, it will be of value to those managing information systems and application development projects in defining the goals they should have in building better systems, and to business owners who are frustrated by their current systems but cannot articulate how or why to change things.ContentsThe “Smart Enough Systems” Manifestoi¾ i¾ i¾ Operational Decisions Are Importanti¾ i¾ i¾ Operational Decisions Can and Should Be Automatedi¾ i¾ i¾ Taking Control of Decisions is Increasingly a Source of Competitive AdvantageThe Need for Smart Enough Systemsi¾ i¾ i¾ The Importance of Operational Decisionsi¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Strategy Drives Decision-makingi¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Strategy Is Not Statici¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Operational Decisions Matteri¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Operational Decisions Are Under Pressurei¾ i¾ i¾ Operational Decision-Making as a Corporate Asseti¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Characteristics of Operational Decisionsi¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Characteristics of Corporate Assetsi¾ i¾ i¾ Introducing Smart Enough Systemsi¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Characteristics of Smart Enough Systemsi¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Current Approaches Faili¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ i¾ Decision Management Is Requiredi¾ i¾ i¾ Introducing Smart Enough Logistics
A novel algorithm for blind channel identification based on modified principle of autocorrelation matching (2003)

A novel algorithm for blind channel identification based on the modified principle of autocorrelation matching is presented. In this algorithm, the channel parameters are decided by solving equations. It can achieve exact identification with no convergence problem. Its persistence to white additive noise is also shown, both in theory and simulation results.
Subaperture correlation based digital adaptive optics for full field optical coherence tomography (2013)

This paper proposes a sub-aperture correlation based numerical phase correction method for interferometric full field imaging systems provided the complex object field information can be extracted. This method corrects for the wavefront aberration at the pupil/ Fourier transform plane without the need of any adaptive optics, spatial light modulators (SLM) and additional cameras. We show that this method does not require the knowledge of any system parameters. In the simulation study, we consider a full field swept source OCT (FF SSOCT) system to show the working principle of the algorithm. Experimental results are presented for a technical and biological sample to demonstrate the proof of the principle.
High-sensitivity miniaturized immunoassays for tumor necrosis factor ? using microfluidic systems (2004)

We use microfluidic chips to detect the biologically important cytokine tumor necrosis factor alpha (TNF- alpha) with picomolar sensitivity using sub-microliter volumes of samples and reagents. The chips comprise a number of independent capillary systems (CSs), each of which is composed of a filling port, an appended microchannel, and a capillary pump. Each CS fills spontaneously by capillary forces and includes a self-regulating mechanism that prevents adventitious drainage of the microchannels. Thus, interactive control of the flow in each CS is easily achieved via collective control of the evaporation in all CSs by means of two Peltier elements that can independently heat and cool. Long incubation times are crucial for high sensitivity assays and can be conveniently obtained by adjusting the evaporation rate to have low flow rates of approximately 30 nL min(-1). The assay is a sandwich fluorescence immunoassay and takes place on the surface of a poly(dimethylsiloxane)(PDMS) slab placed across the microchannels. We precoat PDMS with capture antibodies (Abs), localize the capture of analyte molecules using a chip, then bind the captured analyte molecules with fluorescently-tagged detection Abs using a second chip. The assay results in a mosaic of fluorescence signals on the PDMS surface which are measured using a fluorescence scanner. We show that PDMS is a compatible material for high sensitivity fluorescence assays, provided that detection antibodies with long excitation wavelength fluorophores ( > or =580 nm) are employed. The chip design, long incubation times, proper choice of fluorophores, and optimization of the detection Ab concentration all combine to achieve high-sensitivity assays. This is exemplified by an experiment with 170 assay sites, occupying an area of approximately 0.6 mm(2) on PDMS to detect TNF-alpha in 600 nL of a dendritic cell (DC) culture medium with a sensitivity of approximately 20 pg mL(-1)(1.14 pM).
Virtual typing by people with tetraplegia using a self-calibrating intracortical brain-computer interface (2015)

Brain-computer interfaces (BCIs) promise to restore independence for people with severe motor disabilities by translating decoded neural activity directly into the control of a computer. However, recorded neural signals are not stationary (that is, can change over time), degrading the quality of decoding. Requiring users to pause what they are doing whenever signals change to perform decoder recalibration routines is time-consuming and impractical for everyday use of BCIs. We demonstrate that signal nonstationarity in an intracortical BCI can be mitigated automatically in software, enabling long periods (hours to days) of self-paced point-and-click typing by people with tetraplegia, without degradation in neural control. Three key innovations were included in our approach: tracking the statistics of the neural activity during self-timed pauses in neural control, velocity bias correction during neural control, and periodically recalibrating the decoder using data acquired during typing by mapping neural activity to movement intentions that are inferred retrospectively based on the user's self-selected targets. These methods, which can be extended to a variety of neurally controlled applications, advance the potential for intracortical BCIs to help restore independent communication and assistive device control for people with paralysis.
Host Heterogeneity in Susceptibility and Disease Dynamics: Tests of a Mathematical Model (1997)

Most mathematical models of disease assume that transmission is linearly dependent on the densities of host and pathogen. Recent data for animal diseases, however, have cast doubt on this assumption, without assessing the usefulness of alternative models. In this article, we use a combination of laboratory dose-response experiments, field transmission experiments, and observations of naturally occurring populations to show that virus transmission in gypsy moths is a nonlinear function of virus density, apparently because of heterogeneity among individual gypsy moth larvae in their susceptibility to the virus. Dose-response experiments showed that larvae from a laboratory colony of gypsy moths are substantially less heterogeneous in their susceptibility to the virus than are larvae from feral populations, and field experiments showed that there is a more strongly nonlinear relationship between transmission and virus density for feral larvae than for lab larvae. This nonlinearity in transmission changes the dynamics of the virus in natural populations so that a model incorporating host heterogeneity in susceptibility to the virus gives a much better fit to data on virus dynamics from large-scale field plots than does a classical model that ignores host heterogeneity. Our results suggest that heterogeneity among individuals has important effects on the dynamics of disease in insects at several spatial and temporal scales and that heterogeneity in susceptibility may be of general importance in the ecology of disease.
Rickettsia prowazekiiUses ansn-Glycerol-3-Phosphate Dehydrogenase and a Novel Dihydroxyacetone Phosphate Transport System To Supply Triose Phosphate for Phospholipid Biosynthesis (2010)

Rickettsia prowazekii is an obligate intracellular pathogen that possesses a small genome and a highly refined repertoire of biochemical pathways compared to those of free-living bacteria. Here we describe a novel biochemical pathway that relies on rickettsial transport of host cytosolic dihydroxyacetone phosphate (DHAP) and its subsequent conversion to sn-glycerol-3-phosphate (G3P) for synthesis of phospholipids. This rickettsial pathway compensates for the evolutionary loss of rickettsial glycolysis/gluconeogenesis, the typical endogenous source of G3P. One of the components of this pathway is R. prowazekii open reading frame RP442, which is annotated GpsA, a G3P dehydrogenase (G3PDH). Purified recombinant rickettsial GpsA was shown to specifically catalyze the conversion of DHAP to G3P in vitro. The products of the GpsA assay were monitored spectrophotometrically, and the identity of the reaction product was verified by paper chromatography. In addition, heterologous expression of the R. prowazekii gpsA gene functioned to complement an Escherichia coli gpsA mutant. Furthermore, gpsA mRNA was detected in R. prowazekii purified from hen egg yolk sacs, and G3PDH activity was assayable in R. prowazekii lysed-cell extracts. Together, these data strongly suggested that R. prowazekii encodes and synthesizes a functional GpsA enzyme, yet R. prowazekii is unable to synthesize DHAP as a substrate for the GpsA enzymatic reaction. On the basis of the fact that intracellular organisms often avail themselves of resources in the host cell cytosol via the activity of novel carrier-mediated transport systems, we reasoned that R. prowazekii transports DHAP to supply substrate for GpsA. In support of this hypothesis, we show that purified R. prowazekii transported and incorporated DHAP into phospholipids, thus implicating a role for GpsA in vivo as part of a novel rickettsial G3P acquisition pathway for phospholipid biosynthesis.
Porin mutants with new channel properties (1998)

The general diffusion porin from Rhodopseudomonas blastica was produced in large amounts in Escherichia coli inclusion bodies and (re)natured to the exact native structure. Here, we report on 13 mutants at the pore eyelet giving rise to new diffusion properties as measured in planar lipid bilayer experiments. The crystal structures of seven of these mutants were established. The effects of charge-modifying mutations at the pore eyelet are consistent with the known selectivity for cations. Deletions of 16 and 27 residues of the constriction loop L3 resulted in labile trimers and pores. The reduction of the eyelet cross section by introducing tryptophans gave rise to a closely correlated decrease of the conductivities. A mutant with six newly introduced tryptophans in the eyelet closed its pore in a defined manner within seconds under a voltage of 20 mV, suggesting the existence of two states. The results indicate that the pore can be engineered in a rational manner.
NPS 1506, A Novel NMDA Receptor Antagonist and Neuroprotectant: Review of Preclinical and Clinical Studies (1999)

NPS 1506 is a moderate affinity, uncompetitive N-methyl-D-aspartate (NMDA) receptor antagonist. NPS 1506 is neuroprotective in rodent models of ischemic stroke, hemorrhagic stroke, and head trauma, with a 2-hr window of opportunity. Neuroprotectant doses of NPS 1506 ranged from approximately 0.1-1.0 mg/kg, with peak plasma concentrations ranging from 8-80 ng/mL. Even at doses producing behavioral toxicity, NPS 1506 did not elicit MK-801-like behaviors, did not generalize to phencyclidine (PCP), and did not elicit neuronal vacuolization. In a Phase I study, intravenous (i.v.) doses of NPS 1506 from 5-100 mg were well tolerated and provided plasma concentrations in excess of those required for neuroprotection in rodents. Adverse events at the 100-mg dose included mild dizziness and lightheadedness, and mild to moderate ataxia. Neither PCP-like psychotomimetic effects nor cardiovascular effects were noted. The long plasma half-life of NPS 1506 (approximately 60 hr) suggests that a single i.v. dose will provide prolonged neuroprotection in humans.
GC base sequence recognition by oligoimidazolecarboxamide and C-terminus-modified analogs of distamycin deduced from circular dichroism, proton nuclear magnetic resonance, and methidiumpropylethylenediaminetetraacetate-iron(II) footprinting studies (1993)

The DNA binding properties of a series of imidazole-containing and C-terminus-modified analogues 4-7 of distamycin are described. These analogues contain one to four imidazole units, respectively. Data from the ethidium displacement assay showed that these compounds bind in the minor groove of DNA, with the relative order of binding constants of 6 (Im3) > 7 (Im4) > 5 (Im2) > 4 (Im1). The reduced binding constants of these compounds for poly(dA-dT) relative to distamycin, while they still interact strongly with poly(dG-dC), provided evidence of GC sequence acceptance. The preferences for GC-rich sequences by these compounds were established from a combination of circular dichroism (CD) titration, proton nuclear magnetic resonance (1H-NMR), and methidiumpropylethylenediaminetetraacetate-iron(II) [MPE.Fe-(II)] footprinting studies. In the CD studies, these compounds produced significantly larger DNA-induced ligand bands with poly(dG-dC) than poly(dA-dT) at comparable ligand concentrations. 1H-NMR studies of the binding of 5 to d-[CATGGCCATG]2 provided further evidence of the recognition of GC sequences by these compounds, and suggested that the ligand was located on the underlined sequence in the minor groove with the C-terminus oriented over the T residue. MPE footprinting studies on a GC-rich BamHI/SalI fragment of pBR322 provided unambiguous evidence for the GC sequence selectivity for some of these compounds. Compounds 4 and 7 produced poor footprints on the gels; however, analogues 5 and 6 gave strong footprints.(ABSTRACT TRUNCATED AT 250 WORDS)
Klebsiella pneumoniae 1,3-propanediol:NAD+ oxidoreductase (1987)

Fermentative utilization of glycerol, a more reduced carbohydrate than aldoses and ketoses, requires the disposal of the two extra hydrogen atoms. This is accomplished by sacrificing an equal quantity of glycerol via an auxiliary pathway initiated by glycerol dehydratase. The product, 3-hydroxypropionaldehyde, is then reduced by 1,3-propanediol NAD+:oxidoreductase (1,3-propanediol dehydrogenase; EC 1.1.1.202), resulting in the regeneration of NAD+ from NADH. The pathway for the assimilation of glycerol is initiated by an NAD-linked dehydrogenase. In Klebsiella pneumoniae the two pathways are encoded by the dha regulon which is inducible only anaerobically. In this study 1,3-propanediol:NAD+ oxidoreductase was purified from cells grown anaerobically on glycerol. The enzyme was immunochemically distinct from the NAD-linked glycerol dehydrogenase and was an octamer or hexamer of a polypeptide of 45,000 +/- 3,000 daltons. When tested as a dehydrogenase, only 1,3-propanediol served as a substrate; no activity was detected with ethanol, 1-propanol, 1,2-propanediol, glycerol, or 1,4-butanediol. The enzyme was inhibited by chelators of divalent cations. An enzyme preparation inhibited by alpha,alpha'-dipyridyl was reactivated by the addition of Fe2+ or Mn2+ after removal of the chelator by gel filtration. As for glycerol dehydrogenase, 1,3-propanediol oxidoreductase is apparently inactivated by oxidation during aerobic metabolism, under which condition the enzyme becomes superfluous.
Peptide inhibitors of dengue virus and West Nile virus infectivity (2005)

Viral fusion proteins mediate cell entry by undergoing a series of conformational changes that result in virion-target cell membrane fusion. Class I viral fusion proteins, such as those encoded by influenza virus and human immunodeficiency virus (HIV), contain two prominent alpha helices. Peptides that mimic portions of these alpha helices inhibit structural rearrangements of the fusion proteins and prevent viral infection. The envelope glycoprotein (E) of flaviviruses, such as West Nile virus (WNV) and dengue virus (DENV), are class II viral fusion proteins comprised predominantly of beta sheets. We used a physio-chemical algorithm, the Wimley-White interfacial hydrophobicity scale (WWIHS) in combination with known structural data to identify potential peptide inhibitors of WNV and DENV infectivity that target the viral E protein. Viral inhibition assays confirm that several of these peptides specifically interfere with target virus entry with 50% inhibitory concentration (IC50) in the 10 microM range. Inhibitory peptides similar in sequence to domains with a significant WWIHS scores, including domain II (IIb), and the stem domain, were detected. DN59, a peptide corresponding to the stem domain of DENV, inhibited infection by DENV (>99% inhibition of plaque formation at a concentrations of <25 microM) and cross-inhibition of WNV fusion/infectivity (>99% inhibition at <25 microM) was also demonstrated with DN59. However, a potent WNV inhibitory peptide, WN83, which corresponds to WNV E domain IIb, did not inhibit infectivity by DENV. Additional results suggest that these inhibitory peptides are noncytotoxic and act in a sequence specific manner. The inhibitory peptides identified here can serve as lead compounds for the development of peptide drugs for flavivirus infection.
Considerations in Electrodeposition of Compositionally Modulated Alloys (1990)

High‐quality specimens of sufficient thickness for reliable testing are needed if the enhanced properties observed for ultrastructured multilayered metals are to be understood and exploited. In the present paper, factors affecting the quality of multilayers electrodeposited from a single electrolyte, via concerted modulation of the electrode potential and electrolyte mass transport, are discussed. The importance of precise control of the potential during deposition of the more noble metal is emphasized. Results obtained by a pulse technique show that Ni passivation does not occur under the conditions used to electrodeposit Ni‐Cu multilayers. Attainable deposit quality is illustrated by tensile test data for a series of 90%Ni‐10%Cu specimens that are twice as strong as Ni and for which the standard deviations for the ultimate tensile strength and modulus are only 1.5 and 3.9%, respectively.
Rma1, a novel type of RING finger protein conserved from Arabidopsis to human, is a membrane-bound ubiquitin ligase (2001)

Rma1 is a protein with a RING finger motif and a C-terminal membrane-anchoring domain and is well conserved among higher eukaryotes. We show that fusion proteins between maltose binding protein (MBP) and human or Arabidopsis Rma1 are polyubiquitinated, when incubated with the rabbit reticulocyte or the wheat germ lysate, respectively. The polyubiquitination of MBP-Rma1 has been reconstituted by incubation with purified ubiquitin, the ubiquitin-activating enzyme E1, and one of the two ubiquitin-conjugating E2 enzymes (Ubc4 or UbcH5a). Other E2 enzymes tested, E2-20k, E2-25k, Ubc3 and Ubc8, are not able to confer this modification. Mutational analysis shows that the RING finger motif of Rma1 is necessary for the auto-ubiquitination of MBP-Rma1. Thus, Rma1 represents a novel, membrane-bound type of ubiquitin ligase E3, which probably functions with the Ubc4/5 subfamily of E2. The MBP moiety but not Rma1 itself is ubiquitinated in the auto-ubiquitination reaction of MBP-Rma1. Free MBP in solution is not a substrate of Rma1. These observations indicate that bringing the substrate into its physical vicinity is very important for the action of ubiquitin ligase.