gebhart/patrepeval huggingface dataset:
Microbial d-xylonate production (2012)

d-Xylonic acid is a versatile platform chemical with reported applications as complexing agent or chelator, in dispersal of concrete, and as a precursor for compounds such as co-polyamides, polyesters, hydrogels and 1,2,4-butanetriol. With increasing glucose prices, d-xylonic acid may provide a cheap, non-food derived alternative for gluconic acid, which is widely used (about 80 kton/year) in pharmaceuticals, food products, solvents, adhesives, dyes, paints and polishes. Large-scale production has not been developed, reflecting the current limited market for d-xylonate. d-Xylonic acid occurs naturally, being formed in the first step of oxidative metabolism of d-xylose by some archaea and bacteria via the action of d-xylose or d-glucose dehydrogenases. High extracellular concentrations of d-xylonate have been reported for various bacteria, in particular Gluconobacter oxydans and Pseudomonas putida. High yields of d-xylonate from d-xylose make G. oxydans an attractive choice for biotechnical production. G. oxydans is able to produce d-xylonate directly from plant biomass hydrolysates, but rates and yields are reduced because of sensitivity to hydrolysate inhibitors. Recently, d-xylonate has been produced by the genetically modified bacterium Escherichia coli and yeast Saccharomyces cerevisiae and Kluyveromyces lactis. Expression of NAD+-dependent d-xylose dehydrogenase of Caulobacter crescentus in either E. coli or in a robust, hydrolysate-tolerant, industrial Saccharomyces cerevisiae strain has resulted in d-xylonate titres, which are comparable to those seen with G. oxydans, at a volumetric rate approximately 30 % of that observed with G. oxydans. With further development, genetically modified microbes may soon provide an alternative for production of d-xylonate at industrial scale.
Large expert-curated database for benchmarking document similarity detection in biomedical literature search (2019)

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
High-throughput, label-free, multivariate cell analysis with optofluidic time-stretch microscopy (2017)

We demonstrate a label-free cell analyzer with high throughput and single-cell resolution based on optofluidic time-stretch microscopy. It is capable of acquiring images of cells at a throughput beyond 10,000 cells/s with a spatial resolution of 780 nm in a label-free manner, allowing for statistical analysis of the cells' phenotypes from the images via machine learning methods. Moreover, using compressed sensing, the throughput can be further improved by a factor of 50. Thus, our scheme holds great potential for cell analysis in various scientific and industrial fields, including bio-fuel production and disease evaluation.
Chapter 2. Synthetic methods . Part (iii) Enzyme chemistry (1998)

A. J. Carnell, Annu. Rep. Prog. Chem., Sect. B: Org. Chem., 1998, 94, 39 DOI: 10.1039/OC094039
Inositol 1,4,5-Trisphosphate Directs Ca2+Flow between Mitochondria and the Endoplasmic/Sarcoplasmic Reticulum: A Role in Regulating Cardiac Autonomic Ca2+Spiking (2000)

The signaling role of the Ca(2+) releaser inositol 1,4, 5-trisphosphate (IP(3)) has been associated with diverse cell functions. Yet, the physiological significance of IP(3) in tissues that feature a ryanodine-sensitive sarcoplasmic reticulum has remained elusive. IP(3) generated by photolysis of caged IP(3) or by purinergic activation of phospholipase Cgamma slowed down or abolished autonomic Ca(2+) spiking in neonatal rat cardiomyocytes. Microinjection of heparin, blocking dominant-negative fusion protein, or anti-phospholipase Cgamma antibody prevented the IP(3)-mediated purinergic effect. IP(3) triggered a ryanodine- and caffeine-insensitive Ca(2+) release restricted to the perinuclear region. In cells loaded with Rhod2 or expressing a mitochondria-targeted cameleon and TMRM to monitor mitochondrial Ca(2+) and potential, IP(3) induced transient Ca(2+) loading and depolarization of the organelles. These mitochondrial changes were associated with Ca(2+) depletion of the sarcoplasmic reticulum and preceded the arrest of cellular Ca(2+) spiking. Thus, IP(3) acting within a restricted cellular region regulates the dynamic of calcium flow between mitochondria and the endoplasmic/sarcoplasmic reticulum. We have thus uncovered a novel role for IP(3) in excitable cells, the regulation of cardiac autonomic activity.
Stimulation of the D5 dopamine receptor acidifies the lysosomal pH of retinal pigmented epithelial cells and decreases accumulation of autofluorescent photoreceptor debris (2012)

Optimal neuronal activity requires that supporting cells provide both efficient nutrient delivery and waste disposal. The incomplete processing of engulfed waste by their lysosomes can lead to accumulation of residual material and compromise their support of neurons. As most degradative lysosomal enzymes function best at an acidic pH, lysosomal alkalinization can impede enzyme activity and increase lipofuscin accumulation. We hypothesize that treatment to reacidify compromised lysosomes can enhance degradation. Here, we demonstrate that degradation of ingested photoreceptor outer segments by retinal pigmented epithelial cells is increased by stimulation of D5 dopamine receptors. D1/D5 receptor agonists reacidified lysosomes in cells alkalinized by chloroquine or tamoxifen, with acidification dependent on protein kinase A. Knockdown with siRNA confirmed acidification was mediated by the D5 receptor. Exposure of cells to outer segments increased lipofuscin-like autofluorescence, but SKF 81297 reduced autofluorescence. Likewise, SKF 81297 increased the activity of lysosomal protease cathepsin D in situ. D5DR stimulation also acidified lysosomes of retinal pigmented epithelial cells from elderly ABCA4(-/-) mice, a model of recessive Stargardt's retinal degeneration. In conclusion, D5 receptor stimulation lowers compromised lysosomal pH, enhancing degradation. The reduced accumulation of lipofuscin-like autofluorescence implies the D5 receptor stimulation may enable cells to better support adjacent neurons.
The First Regiospecific, Enantiospecific Total Synthesis of 6-Oxoalstophylline and an Improved Total Synthesis of Alstonerine and Alstophylline as Well as the Bisindole Alkaloid Macralstonine (2005)

A Wacker sequence has been modified to rapidly generate ring E of (-)-alstonerine, (+)-6-oxoalstophylline, and (-)-alstophylline via a domino process. This one-pot sequence provides facile entry into the dihydropyranyl enone unit of many Alstonia alkaloids. [structure: see text]
Improvements in epitaxial lateral overgrowth of InP by MOVPE (2014)

Indium phosphide and silicon play important and complementary roles in communications wavelength photonic devices. Realizing high quality coalesced epitaxial lateral overgrown (ELO) InP films on Si could greatly reduce cost and encourage the proliferation of energy efficient photonic integrated circuits in consumer devices. By adjusting a parallel line ELO mask and metalorganic vapor phase epitaxial growth conditions, we have fully coalesced and partially coalesced epitaxial lateral overgrowth of InP on InP substrates and Si substrates having strain relaxed III/V buffer layers, respectively. Extended defects were investigated using transmission electron microscopy and were not found to originate at the coalescence of the nearest neighbor growth fronts for linear parallel growth windows oriented 60° off of [0−11] when using a high V/III ratio of 406. In addition, narrowly separated linear parallel growth windows having a large aspect ratio of 7.5 were seen to inhibit the upward propagation of stacking faults through several neighboring openings. Elimination of these two defect sources would leave primarily the challenge of optimizing the morphology of the overgrown InP as a substantial barrier to achieving coalesced ELO InP of sufficient quality for photonic device applications.
[New concept of glaucoma. Primarily an optic neuropathy, not a disease of the anterior chamber angle]. (1999)

Glaucoma is now considered to be primarily an optic neuropathy, not a disease of the anterior chamber angle. Although intraocular pressure remains a crucial variable, the relationship between increased intraocular pressure and glaucoma is now recognised as being less simple than formerly believed. The new approach to the disease is reflected in a review by the National Board of Health and Welfare of the most recent advances in our knowledge of open-angle glaucoma, advances made possible by improvements in diagnostics and epidemiology. The prognosis of glaucoma is considerably better than often appreciated, by the profession and by the general public.
Effects of a pyridine derivative thromboxane synthetase inhibitor and its inactive isomer in endotoxic shock in the rat (1983)

1 We investigated the effects of a pyridine derivative thromboxane synthetase inhibitor and its inactive ortho isomer on arachidonic acid metabolism and pathophysiological sequelae of endotoxic shock. In vehicle-treated rats, 30 min after intravenous S. enteritidis endotoxin (15 mg/kg), plasma iTxB2 (the stable metabolite of thromboxane A2) increased from non-detectable levels (less than 100 pg/ml) to 763 +/- 250 pg/ml (n = 10). Plasma i6-keto-PGF1 alpha (the stable metabolite of prostacyclin, PGI2) increased to 1850 +/- 426 pg/ml, (n = 9) and plasma iPGE increased to 2350 = 560 (n = 5). Pretreatment with the pyridine active (PA) meta isomer (30 mg/kg i.p.) significantly (P less than 0.05) suppressed iTxB2 to 390 +/- 31 pg/ml (n = 10) although 6-keto-PGF1 alpha levels (1294 +/- 358 pg/ml, n = 5) and plasma iPGE (2847 +/- 1103 pg/ml, n = 5) were not significantly different from the shocked control values. In contrast, pretreatment with, the pyridine inactive (PI) ortho isomer did not significantly affect endotoxin-induced iTxB2 (1431 +/- 194 pg/ml, n = 5) or i6-keto-PGF1 alpha synthesis (628 +/- 266 pg/ml, n = 5). 2 Pretreatment of rats with the Tx synthetase inhibitor, PA, significantly enhanced (P less than 0.05) survival and prevented splanchnic infarction relative to both endotoxin shocked control rats and those pretreated with the PI isomer. 3 Significantly reduced lysosomal labilization, hepatocellular dysfunction and elevations in serum fibrin/fibrinogen degradation products were seen only in groups pretreated with the PA isomer. 4 The beneficial effects of the latter compound in endotoxic shock thus appear to be due to inhibition of Tx synthesis, since its ortho isomer did not inhibit TxA2 synthesis nor did it protect against endotoxic shock.
Versatility of the adenovirus-vectored foot-and-mouth disease vaccine platform across multiple foot-and-mouth disease virus serotypes and topotypes using a vaccine dose representative of the AdtA24 conditionally licensed vaccine (2018)

We investigated the serotype- and topotype versatility of a replication-deficient human adenovirus serotype 5 vectored foot-and-mouth disease (FMD) vaccine platform (AdtFMD). Sixteen AdtFMD recombinant subunit monovalent vaccines targeting twelve distinct FMD virus (FMDV) serotype/topotypes in FMD Regional Pools I-VII were constructed. The AdtA24 serotype conditionally licensed vaccine served as the basis for vaccine design and target dose for cattle clinical trials. Several vaccines contained an additional RGD motif genetic insertion in the adenovector fiber knob, and/or a full-length 2B gene insertion in the FMDV P1 gene cassette. In 13 of the 22 efficacy studies conducted, naïve control and AdtFMD vaccinated cattle were challenged intradermolingually at 2 weeks post-vaccination using a FMDV strain homologous to the AdtFMD vaccine strain. Each of the 16 AdtFMD vaccines were immunogenic based on the presence of homologous neutralizing antibodies in the serum of approximately 90% of total vaccinates (n = 375) on the day of challenge. Importantly, for 75% of vaccines tested, the effective dose that conferred 100% protection against clinical FMD was identical to or in some cases lower than, the minimum protective dose for the conditionally licensed AdtA24 vaccine formulated with ENABL® adjuvant. Results also confirmed the capability of the AdtFMD vaccine platform to differentiate infected from vaccinated animals (DIVA) across the five FMDV serotypes evaluated. Collectively, this comprehensive set of FMD cattle vaccine dose ranging studies highlights the serotype- and topotype versatility of the AdtFMD vaccine platform for further development, licensure, and application in FMD outbreak control and disease eradication efforts.
On the Asymptotic Performance of Multiple Antenna Channels with Fast Channel Feedback (2006)

In this paper, we analyze the asymptotic performance of multiple antenna channels where the transmitter has either perfect or finite bit channel state information. Using the diversity-multiplexing tradeoff to characterize the system performance, we demonstrate that channel feedback can fundamentally change the system behavior. Even one-bit of information can increase the diversity order of the system compared to the system with no transmitter information. In addition, as the amount of channel information at the transmitter increases, the diversity order for each multiplexing gain increases and goes to infinity for perfect transmitter information. The major reason for diversity order gain is a "location-dependent" temporal power control, which adapts the power control strategy based on the average channel conditions of the channel.
Repeatability in Ferrite Nanoparticle Synthesis. (2021)

Abstract not provided.
AugCogifying the Army's Future Warfighter (2005)

The U.S. Army wants to ensure that the Future Force Warrior (FFW) will see first, understand first, act first and finish decisively as the means to tactical success. The Army of the future conceives of small combat units with netted communications enhanced with information from distributed and fused sensors, tactical intelligent assets enabling increased situation assessment, and on-the-move planning (FFW, 2004). The increase in information flow won’t come without a cost, however. Information management will be a key aspect of this distributed system. The availability of such technologies as Augmented Cognition (AugCog), will allow the system to be tailored to the situational and cognitive needs of the warfighter. This paper describes an example of AugCog technology applied to a Communications System.
Effect of Temperature on Salt Diffusion into Vegetable Tissue (2011)

The diffusion process has many applications in food processing operations, such as extraction; preservation (curing, salting, and smoking); drying; and color transfer. Our main objective was to measure the diffusion coefficient, Ds, of salt into vegetable tissue (celery, mushroom, and water chestnut) as a function of temperature. For this purpose, a sample of tissue was used to separate donor and receiver compartments, each with solutions of different salt concentrations. Values of Ds were determined by periodic monitoring. The results show that the equilibrium distribution coefficient, K, and Ds of all materials were significantly affected by temperature (p < 0.05). The temperature dependence of Ds for all three materials was described by the Arrhenius equation, with water chestnut showing the lowest activation energy.
Innate and acquired immunity in neurodegenerative disorders (1999)

Journal of Leukocyte BiologyVolume 65, Issue 4 p. 407-408 Journal ArticleFree Access Innate and acquired immunity in neurodegenerative disorders Howard E. Gendelman, Corresponding Author Howard E. Gendelman hegendel@mail.unmc.edu The Center for Neurovirology and Neurodegenerative Disorders, the Departments of Pathology and Microbiology and Psychiatry, University of Nebraska Medical Center, OmahaCorrespondence: Howard E. Gendelman, M.D., Center for Neurovirology and Neurodegenerative Disorders, University of Nebraska Medical Center, 985215 Nebraska Medical Center, Omaha, NE 68198-5215. E-mail: hegendel@mail.unmc.eduSearch for more papers by this authorDavid G. Folks, David G. Folks The Center for Neurovirology and Neurodegenerative Disorders, the Departments of Pathology and Microbiology and Psychiatry, University of Nebraska Medical Center, OmahaSearch for more papers by this author Howard E. Gendelman, Corresponding Author Howard E. Gendelman hegendel@mail.unmc.edu The Center for Neurovirology and Neurodegenerative Disorders, the Departments of Pathology and Microbiology and Psychiatry, University of Nebraska Medical Center, OmahaCorrespondence: Howard E. Gendelman, M.D., Center for Neurovirology and Neurodegenerative Disorders, University of Nebraska Medical Center, 985215 Nebraska Medical Center, Omaha, NE 68198-5215. E-mail: hegendel@mail.unmc.eduSearch for more papers by this authorDavid G. Folks, David G. Folks The Center for Neurovirology and Neurodegenerative Disorders, the Departments of Pathology and Microbiology and Psychiatry, University of Nebraska Medical Center, OmahaSearch for more papers by this author First published: 01 April 1999 https://doi.org/10.1002/jlb.65.4.407Citations: 15AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article.Citing Literature Volume65, Issue4April 1999Pages 407-408 RelatedInformation
Protection Strategies Enable Selective Conversion of Biomass (2020)

Selective and economic conversion of lignocellulosic biomass components to bio-based fuels and chemicals is the major goal of biorefineries, but low yields and selectivity for fuel precursors such as sugars, furanics, and lignin-derived monomers pose significant disadvantages in process economics. In this Minireview we summarize the existing protection strategies used in biomass chemocatalytic conversion processes and focus the discussions on the mechanisms, challenges, and opportunities of each strategy. We introduce a concept of using analogous methods to manipulate biomass catalytic conversion pathways during the upgrading of carbohydrates to fuels and chemicals. This Minireview may provide new insights into the development of selective biorefining processes from a different perspective, expanding the options for selective conversion of biomass to fuels and chemicals.
Use of Wide-Host-Range Bacteriophages toReduce Salmonella on Poultry Products (2007)

Bacteriophages used to treat infections are typically amplified in a pathogenic host. However, this practice introduces the risk of administering any remaining bacteriophage-resistant pathogen during bacteriophage application if separation techniques are less than perfect. In this study, bacteriophage isolates capable of replicating in both Salmonella and Klebsiella oxytoca were identified and applied to poultry carcasses. These Wide-Host-Range bacteriophages (WHR) were amplified using the non-pathogenic bacteria, Klebsiella oxytoca in tryptic soy broth until a titer of approximately 10⁹ PFU/mL was obtained. WHR and Klebsiella oxytoca were not separated prior to treatment of carcasses. Fresh processed chicken carcasses were inoculated with either Salmonella enteritidis (SE) or S. typhimurium (ST), sprayed with 5 mL of WHR and rinsed with sterile water. Samples were enriched, plated on XLD agar and evaluated for Salmonella-typical colonies. In four separate trials, WHR significantly reduced the recovery of SE. No SE was detected in two trials and a greater than 70% reduction was seen in the other two trials. ST was also significantly reduced in the two trials in which it was included (p<0.05). These experiments suggest that WHR could be an inexpensive and safe method for the reduction of Salmonella on broiler carcasses.
High Power Side-Pumped Yb: YAG Composite Disk Laser (2005)

Thin disk geometry for laser active medium has advantages for high-average-power operation with good beam quality. However it is difficult to obtain high pumping efficiency due to the small thickness of the crystal. To improve the pumping efficiency, we have developed a side-pumped Yb: YAG/YAG composite disk laser with a stacked-LD tight-focusing technique. The maximum output power was 235-W from one disk with the optical efficiency of 0.38.
Potential Causes of Loss of Reduction in Supracondylar Humerus Fractures (2014)

Retrospective study; level II.
<title>Polarization aberrations of crossed folding mirrors</title> (1995)

Polarization aberrations due to varying polarization state across the field of view (FOV) are investigated for crossed folding mirrors. We define crossed mirrors as oriented in space such that s-polarized light incident on the first mirror is p-polarized at the second mirror. This completely compensates for polarization state changes at one point in the field of view. The resulting polarization aberrations are explored across the FOV using the example of aluminum mirrors overcoated with a 12 layer, highly reflective, dielectric stack. The polarization aberration is very low along a band across the field of view. For arbitrary points in the FOV, the retardance and diattenuation are slightly elliptical.
A convex optimisation approach to traffic signal control (2016)

We revisit the problem of traffic signal control in urban traffic networks. Recent work in the literature has studied the use of scheduling algorithms from communication networks to traffic signal control with the aim of maximising the network throughput. However, these algorithms are unable to capture some of the network characteristics such as protocol constraints or penalties on the control actions, e.g. the loss time when changing between phases. In this paper, we propose a convex optimisation approach to traffic signal control that decouples the stability of the system from the choice of traffic control policy. As a result, we are able to design a range of traffic signal control policies that maximise the network throughput, and that at the same time, capture the characteristics of urban traffic networks more accurately.