gebhart/patrepeval huggingface dataset:
Disulfide Bond Formation System in Escherichia coli (2009)

The biological kingdoms have evolved elaborate systems that ensure the catalysis of protein disulfide bond (dsb) formation in the cell. Coexisting in the periplasm of Escherichia coli are the DsbA-DsbB disulfide-introducing and DsbC-DsbD disulfide-isomerizing pathways, which promote the oxidative folding of secreted proteins. Recent structural studies of DsbB have illuminated conformational dynamics involved in the effective oxidation of the extremely reduction-prone oxidase, DsbA, as well as the structure of the reaction centre involved in protein Dsb formation de novo in conjunction with ubiquinone. Extensive genetic and biochemical analysis has recently provided insight into how DsbD transports electrons from cytosolic thioredoxin to periplasmic DsbC. To a great extent, the molecular mechanisms of the Dsb enzyme system in E. coli have been elucidated, and are applicable to the study of protein disulfide formation systems in other organisms.
Data cache management using frequency-based replacement (1990)

We propose a new frequency-based replacement algorithm for managing caches used for disk blocks by a file system, database management system, or disk control unit, which we refer to here as data caches. Previously, LRU replacement has usually been used for such caches. We describe a replacement algorithm based on the concept of maintaining reference counts in which locality has been “factored out”. In this algorithm replacement choices are made using a combination of reference frequency and block age. Simulation results based on traces of file system and I/O activity from actual systems show that this algorithm can offer up to 34% performance improvement over LRU replacement, where the improvement is expressed as the fraction of the performance gain achieved between LRU replacement and the theoretically optimal policy in which the reference string must be known in advance. Furthermore, the implementation complexity and efficiency of this algorithm is comparable to one using LRU replacement.
Active axial eye motion tracking by extended range, closed loop OPD-locked white light interferometer for combined confocal/ en face optical coherence tomography imaging of the human eye fundus in vivo (2009)

We report an active tracking device based on white light coherence ranging using a spectrally interrogated Michelson interferometer, which is used to monitor and correct for the axial displacement of the eye and head of the subject in a confocal scanning ophthalmoscope/en face OCT system (SLO/OCT). The Nyquist limit range of the spectrometer in the tracking interferometer is ~5.4 mm, which is adequate for monitoring the axial position of axially extended layered objects like the human eye fundus. Both the tracking and imaging interferometers share the eye interface optics and the sample and also an optical path (OPD) changing device in the reference (fast voice coil mounted retroreflector), that keeps them locked at constant OPD values. As a consequence, the sensitivity of the tracking interferometer is not affected by the spectrometer sensitivity roll-off with increased OPD and mirror term ambiguity tracking errors close to OPD = 0 are eliminated. Moreover, the axial tracking range is only limited by the voice coil stage travel range. A real time data acquisition processor board is used to digitize the spectrometer signal and calculate the correction signal applied to the voice coil with an update time better than 5 ms. We demonstrate axial motion corrected combined confocal/en face OCT imaging of the human eye fundus in vivo.
Comparative Genomic Analysis of Three Strains of Ehrlichia ruminantium Reveals an Active Process of Genome Size Plasticity (2006)

Ehrlichia ruminantium is the causative agent of heartwater, a major tick-borne disease of livestock in Africa that has been introduced in the Caribbean and is threatening to emerge and spread on the American mainland. We sequenced the complete genomes of two strains of E. ruminantium of differing phenotypes, strains Gardel (Erga; 1,499,920 bp), from the island of Guadeloupe, and Welgevonden (Erwe; 1,512,977 bp), originating in South Africa and maintained in Guadeloupe in a different cell environment. Comparative genomic analysis of these two strains was performed with the recently published parent strain of Erwe (Erwo) and other Rickettsiales (Anaplasma, Wolbachia, and Rickettsia spp.). Gene order is highly conserved between the E. ruminantium strains and with A. marginale. In contrast, there is very little conservation of gene order with members of the Rickettsiaceae. However, gene order may be locally conserved, as illustrated by the tuf operons. Eighteen truncated protein-encoding sequences (CDSs) differentiate Erga from Erwe/Erwo, whereas four other truncated CDSs differentiate Erwe from Erwo. Moreover, E. ruminantium displays the lowest coding ratio observed among bacteria due to unusually long intergenic regions. This is related to an active process of genome expansion/contraction targeted at tandem repeats in noncoding regions and based on the addition or removal of ca. 150-bp tandem units. This process seems to be specific to E. ruminantium and is not observed in the other Rickettsiales.
Adrenal catecholamine output in response to stimulation of the splanchnic nerve in bursts in the conscious calf. (1982)

1. Different patterns of stimulation have been applied to the peripheral end of the right splanchnic nerve, below behavioural threshold, in conscious 2-5 week-old calves. 2. The effects of continuous stimulation at 4 Hz for 10 min were compared with those of stimulation at 40 Hz in 1 s bursts at 10 s intervals for the same period. Delivering the same total number of impulses in the form of bursts in this way increased the output of both adrenaline and noradrenaline and this increase was statistically significant in the case of adrenaline (P less than 0.02) but not noradrenaline. 3. The effects of stimulation in 1 s bursts at 10 s intervals for 2-3 min were investigated over the frequency range 10-150 Hz and compared with the effects of continuous stimulation over the range 1-15 Hz obtained previously in conscious calves of the same age (Edwards, Furness and Halle, 1980). The output of adrenaline but not noradrenaline was found to significantly greater in response to stimulation in bursts at frequencies of up to 40 Hz than when the equivalent number of impulses were delivered at a constant rate (P less than 0.02). 4. It is concluded that the release of catecholamines from the adrenal gland is maximal at relatively high frequencies (40-100 Hz) when the impulses are delivered in bursts.
A mechanism for the dynamic construction of clusters using active networks (2002)

In this paper we describe an active networks framework for dynamically constructing clusters in response to user requests for computational service. Active network nodes match requests for computational service to appropriate offers of such service using recent access and predicted usage pattern information to construct clusters on-demand. The active networks approach exploits the fact that network devices are in an ideal position to decide which resources should be combined to build clusters in response to particular requests. This approach offers advantages in terms of anonymity of service (systems are unaware of one anothers' existence), scalability (scheduling is distributed across many network processors), fault tolerance (service is distributed so failures are recoverable and/or localized) and automatic localization (clusters are created as close to the requester as possible).
Microbial synthesis of triacetic acid lactone (2005)

Native g2ps1-encoded 2-pyrone synthase (2-PS) from Gerbera hybrida, a mutant Brevibacterium ammoniagenes fatty acid synthase B (FAS-B) and two different mutants of Penicillium patulum 6-methylsalycilic acid synthase (6-MSAS) are examined to identify the best enzyme to recruit for the microbial synthesis of triacetic acid lactone (TAL). To identify the best microbial host for these evaluations, the native TAL-synthesizing activity of g2ps1-encoded 2-PS is expressed in recombinant Escherichia coli and Saccharomyces cerevisiae constructs. Five-fold higher expression levels of 2-PS are observed in S. cerevisiae. Consequently, microbial synthesis of TAL focuses on S. cerevisiae constructs. Comparison of different promoters for the expression of g2ps1 in S. cerevisiae indicates that the alcohol dehydrogenase II promoter (P(ADH2)) affords the highest expression levels of 2-PS. As a result, the genes encoding the various TAL-synthesizing enzyme activities are expressed in S. cerevisiae from a P(ADH2) promoter. To extend TAL-synthesizing activity beyond g2ps1-encoded 2-PS, the ketoreductase domains of fasB-encoded FAS-B and 6-MSAS-encoded 6-MSAS are modified using a single mutation. Modification of the nicotinamide cofactor-binding site of 6-MSAS with a triple mutation is also examined. Separate S. cerevisiae constructs expressing native g2ps1, mutant Y2226F fasB, mutant Y1572F 6-MSAS, and mutant G1419A-G1421P-G1424A 6-MSAS are cultured under the same fermentor-controlled conditions. The highest concentration (1.8 g/L) and yield (6%) of TAL are synthesized from glucose by S. cerevisiae expressing the Y1572F mutant of 6-MSAS.
How We Localize Sound (1999)

For as long as we humans have lived on Earth, we have been able to use our ears to localize the sources of sounds. Our ability to localize warns us of danger and helps us sort out individual sounds from the usual cacophony of our acoustical world. Characterizing this ability in humans and other animals makes an intriguing physical, physiological, and psychological study (see figure 1).
Enhancement mechanisms for optical forces in integrated optics (2006)

We investigate the extension of optical micromanipulation to integrated optics. In particular, we consider whether propagating light signals can cause mechanical reconfiguration of a device. While such forces are intrinsically weak, we predict theoretically that significant displacements can be achieved using various enhancement mechanisms. These include the use of high-index materials, high-<i>Q</i> (cavity quality factor) enhancement, and slow light in photonic crystals. Silicon optical waveguides have a considerable refractive index contrast with the surrounding air, with a ratio of roughly 3.45/1 at optical communications wavelengths. We show that the strong confinement of light to silicon magnifies optical forces arising from overlap in the guided modes of neighboring waveguides. Silica microsphere resonators are known to have extremely high cavity quality factors, in excess of 10<sup>8</sup>. We show that the quality factor of the resonator magnifies the optical force due to modal overlap between two neighboring spheres. Thirdly, we investigate slow-light enhancement of optical forces using photonic-crystal devices. We show that slow-light velocities give rise to larger forces for the same amount of signal power, enhancing optomechanical coupling effects. In addition to being of fundamental interest, our work suggests that optical manipulation may ultimately provide a route to all-optical conformational control and switching.
Identification of the keratan sulfate attachment sites on bovine fibromodulin (1990)

The small keratan sulfate-substituted proteoglycan (fibromodulin) from articular cartilage was shown to contain keratan sulfate linked to the core protein through N-glycosidic linkages to residues Asn-109, Asn-147, Asn-182, and Asn-272. Biosynthetic experiments with articular chondrocytes in the presence of tunicamycin, an inhibitor of N-linked oligosaccharide synthesis, demonstrated a specific inhibition of [35S]SO4 incorporation into fibromodulin. Under the same conditions no effect on the addition of keratan sulfate to the large aggregating proteoglycan was detected. Fibromodulin substituted with keratan sulfate was purified from bovine articular cartilage extracts by density gradient centrifugation, ion-exchange chromatography, and gel-permeation chromatography. Isolation of glycosylated peptides from tryptic digests of fibromodulin by ion-exchange chromatography and reversed-phase high performance liquid chromatography revealed four separate hexosamine-rich species, that were also immunoreactive with monoclonal antibody 5D4. Sequence analysis of these glycopeptides gave blank cycles at positions which corresponded to Asn followed by X-Ser/Thr in the sequence derived from cDNA (Oldberg, A., Antonsson, P., Lindblom, K., and Heinegard, D. (1989) EMBO J. 8, 2601-2604). Hence, all four Asn residues in the leucine-rich region of the fibromodulin core protein can serve as acceptor sites for keratan sulfate addition.
ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells (2014)

With the notable exception of B-cell malignancies, the efficacy of chimeric antigen receptor (CAR) T cells has been limited, and CAR T cells have not been shown to expand and persist in patients with nonlymphoid tumors. Here we demonstrate that redirection of primary human T cells with a CAR containing the inducible costimulator (ICOS) intracellular domain generates tumor-specific IL-17-producing effector cells that show enhanced persistence. Compared with CARs containing the CD3ζ chain alone, or in tandem with the CD28 or the 4-1BB intracellular domains, ICOS signaling increased IL-17A, IL-17F, and IL-22 following antigen recognition. In addition, T cells redirected with an ICOS-based CAR maintained a core molecular signature characteristic of TH17 cells and expressed higher levels of RORC, CD161, IL1R-1, and NCS1. Of note, ICOS signaling also induced the expression of IFN-γ and T-bet, consistent with a TH17/TH1 bipolarization. When transferred into mice with established tumors, TH17 cells that were redirected with ICOS-based CARs mediated efficient antitumor responses and showed enhanced persistence compared with CD28- or 4-1BB-based CAR T cells. Thus, redirection of TH17 cells with a CAR encoding the ICOS intracellular domain is a promising approach to augment the function and persistence of CAR T cells in hematologic malignancies.
Efficient Photocatalysts for CO2 Reduction (2015)

Three types of photocatalytic systems for CO2 reduction, which were recently developed in our group, are reviewed. First, two-component systems containing different rhenium(I) complexes having different roles; i.e., redox photosensitizer and catalyst in the reaction solution are described. The mixed system of a ring-shaped rhenium(I) trinuclear complex and fac-[Re(bpy)(CO)3(MeCN)](+) is currently the most efficient photocatalytic system for CO2 reduction (ΦCO = 0.82 at λex = 436 nm). The second is a series of supramolecular photocatalysts, which have units with different functions in one molecule, i.e., redox photosensitizer, catalyst, and bridging ligand. The highest durability and speed of photocatalysis were achieved by using this system (ΦCO = 0.45, TONCO = 3029, and TOFCO = 35.7 min(-1)). The third is a novel type of artificial Z-Scheme photocatalyst for CO2 reduction, of which photocatalysis is revealed by stepwise excitation of both a semiconductor photocatalyst unit and the supramolecular photocatalyst unit. This system has both strong oxidation and reduction powers.
ChemInform Abstract: Pyrrolooctahydroisoquinolines as Potent and Selective δ Opioid Receptor Ligands: SAR Analysis and Docking Studies. (1998)

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.
Structure and Function of Natural Killer Cell Receptors: Multiple Molecular Solutions to Self, Nonself Discrimination (2002)

In contrast to T cell receptors, signal transducing cell surface membrane molecules involved in the regulation of responses by cells of the innate immune system employ structures that are encoded in the genome rather than generated by somatic recombination and that recognize either classical MHC-I molecules or their structural relatives (such as MICA, RAE-1, or H-60). Considerable progress has recently been made in our understanding of molecular recognition by such molecules based on the determination of their three-dimensional structure, either in isolation or in complex with their MHC-I ligands. Those best studied are the receptors that are expressed on natural killer (NK) cells, but others are found on populations of T cells and other hematopoietic cells. These molecules fall into two major structural classes, those of the immunoglobulin superfamily (KIRs and LIRs) and of the C-type lectin-like family (Ly49, NKG2D, and CD94/NKG2). Here we summarize, in a functional context, the structures of the murine and human molecules that have recently been determined, with emphasis on how they bind different regions of their MHC-I ligands, and how this allows the discrimination of tumor or virus-infected cells from normal cells of the host.
Trigeminal neuralgia: current treatments and future developments (2003)

Trigeminal neuralgia is a rare condition in which patients experience brief, unilateral recurrent episodes of sharp paroxysms of pain that can occur spontaneously or be induced by physical triggers. Although current pharmacotherapy allows most patients at least some degree of comfort, there remains a substantial number who do not have adequate pain management. This can arise as a consequence of the disorder proving to be refractory to drug treatment in an individual, or the manifestation of drug-related side effects at therapeutic doses. When this occurs, the only treatment option is a surgical procedure, which may vary in its level of invasiveness and effect. Therefore, there is a substantial need for new antineuralgic drugs. The aim of this review is to highlight the current pharmacotherapies and those emerging drug treatments which will invariably enhance the treatment options of patients with trigeminal neuralgia.
Manure and Fertilizer Effects on Carbon Balance and Losses for Irrigated Corn (2014)

Little is known about inorganic fertilizer or manure effects on organic carbon (OC) and inorganic C (IC) losses from a furrow irrigated field, particularly in the context of other system C gains or losses. In 2003 and 2004, we measured dissolved organic and inorganic C (DOC, DIC), particulate OC and IC (POC, PIC) concentrations in irrigation inflow, runoff, and percolation waters (6-7 irrigations/y); C inputs from soil amendments and crop biomass; harvested C; and gaseous C emissions from field plots cropped to silage corn (Zea mays L.) in southern Idaho. Annual treatments included: (M) 13 (y 1) and 34 Mg/ha (y 2) stockpiled dairy manure; (F) 78 (yr 1) and 195 kg N/ha (y 2) inorganic N fertilizer; or (NA) no amendment--control. The mean annual total C input into M plots averaged 16.1 Mg/ha, 1.4-times greater than that for NA (11.5 Mg/ha) or F (11.1 Mg/ha), while total C outputs for the three treatments were similar, averaging 11.8 Mg/ha. Thus, the manure plots ended each growing season with an average net gain of 3.8 Mg C/ha (a positive net C flux), while the control (-0.5 Mg C/ha) and fertilizer (-0.4 Mg C/ha) treatments finished the season with a net C loss. Atmospheric CO2 incorporated into the crop biomass contributed 96% of the mean annual C input to NA and F plots but only 68% to M plots. We conclude that nutrient amendments substantially influence the short-term carbon balance of our furrow-irrigated system. Amendments had both direct and indirect influences on individual C components, such as the losses of DIC and POC in runoff and DOC in percolation water, producing temporally complex outcomes which may depend on environmental conditions external to the field.
Electron-transport components of the 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine Δ12-desaturase (Δ12-desaturase) in microsomal preparations from developing safflower (Carthamus tinctorius L.) cotyledons (1990)

The major cytochrome in microsomal membrane preparations from developing seeds of safflower (Carthamus tinctorius, var High Linoleate), has a reduced-minus-oxidized difference spectrum characteristic of a b-type cytochrome, and was identified from its midpoint-potential (E'7.2) value as cytochrome b5. Cytochromes P-450 and P-420 were also present. The cytochrome b5 content of microsomal preparations from a number of oilseed species was found to be in the order of 200-300 pmol/mg of protein. The cytochrome b5 was reduced in the membrane preparations by NADH, demonstrating the presence of an NADH: cytochrome b5 reductase; NADPH was a less effective donor. Microsomal membranes catalysed the NAD(P)H-dependent conversion of radioactive oleate into linoleate, indicating acyl-CoA: lysophosphatidylcholine acyltransferase and 1-acyl-2-oleoyl-sn-glycero-3-phosphocholine delta 12-desaturase (delta 12-desaturase) activity. Desaturation of oleate to linoleate was unaffected by CO, but inhibited by CN-. The addition of oleoyl-CoA to the NADH-reduced membranes resulted in the CN(-)-sensitive partial re-oxidation of cytochrome b5, indicating that electrons from NADH were transferred to the site of desaturation via this cytochrome. The delta 12-desaturase in safflower, therefore, is CN(-)-sensitive and appears to require cytochrome b5 and NADH: cytochrome b5 reductase for activity.
Use of Subatmospheric Pressure to Prevent Progression of Partial-Thickness Burns in a Swine Model (1999)

The poorly understood, complex series of events that follows thermal injury frequently results in progressive loss of tissue. The concept of reversing this distinctive series of events has focused on the zone of stasis. Tissues in the zone of stasis that surround burn injuries usually die over a period of 48 to 72 hours postinjury, resulting in a more severe injury. Application of a controlled subatmospheric pressure (125 mm Hg) in an artificially closed space to partial-thickness burns in pigs significantly decreased the maximum depth of cellular death under the burn when the pressure was applied within 12 hours after burn creation (depth of control burns = 0.885 +/- 0.115 mm; subatmospheric pressure treated burns (0-hour delay) = 0.095 +/- 0.025 mm). A decrease in the depth of cell death was noted when subatmospheric pressure was applied for as little as 6 hours. In summary, the application of the negative pressure to partial-thickness burn injuries prevented progression of the wound to a deeper injury in this experimental pig model. A 12-hour working window exists between injury and treatment with reduced pressure, with an application time of as little as 6 hours for successful prevention of injury progression. This technique may represent a new, inexpensive, 'low tech' method for the treatment of partial-thickness burn injuries.