gebhart/patrepeval huggingface dataset:
Probing the Molecular Basis of Substrate Specificity, Stereospecificity, and Catalysis in the Class II Pyruvate Aldolase, BphI (2011)

BphI, a pyruvate-specific class II aldolase found in the polychlorinated biphenyls (PCBs) degradation pathway, catalyzes the reversible C-C bond cleavage of (4S)-hydroxy-2-oxoacids to form pyruvate and an aldehyde. Mutations were introduced into bphI to probe the contribution of active site residues to substrate recognition and catalysis. In contrast to the wild-type enzyme that has similar specificities for acetaldehyde and propionaldehyde, the L87A variant exhibited a 40-fold preference for propionaldehyde over acetaldehyde. The specificity constant of the L89A variant in the aldol addition reaction using pentaldehyde is increased ∼50-fold, making it more catalytically efficient for pentaldehyde utilization compared to the wild-type utilization of the natural substrate, acetaldehyde. Replacement of Tyr-290 with phenylalanine or serine resulted in a loss of stereochemical control as the variants were able to utilize substrates with both R and S configurations at C4 with similar kinetic parameters. Aldol cleavage and pyruvate α-proton exchange activity were undetectable in the R16A variant, supporting the role of Arg-16 in stabilizing a pyruvate enolate intermediate. The pH dependence of the enzyme is consistent with a single deprotonation by a catalytic base with pK(a) values of approximately 7. In H20A and H20S variants, pH profiles show the dependence of enzyme activity on hydroxide concentration. On the basis of these results, a catalytic mechanism is proposed.
SDSF : social-networking trust based distributed data storage and co-operative information fusion. (2014)

As of 2014, about 2.5 quintillion bytes of data are created each day, and 90% of the data in the world was created in the last two years alone. The storage of this data can be on external hard drives, on unused space in peer-to-peer (P2P) networks or using the more currently popular approach of storing in the Cloud. When the users store their data in the Cloud, the entire data is exposed to the administrators of the services who can view and possibly misuse the data. With the growing popularity and usage of Cloud storage services like Google Drive, Dropbox etc., the concerns of privacy and security are increasing. Searching for content or documents, from this distributed stored data, given the rate of data generation, is a big challenge. Information fusion is used to extract information based on the query of the user, and combine the data and learn useful information. This problem is challenging if the data sources are distributed and heterogeneous in nature where the trustworthiness of the documents may be varied. This thesis proposes two innovative solutions to resolve both of these problems. Firstly, to remedy the situation of security and privacy of stored data, we propose an innovative Social-based Distributed Data Storage and Trust based co-operative Information Fusion Framework (SDSF). The main objective is to create a framework that assists in providing a secure storage system while not overloading a single system using a P2P like approach. This framework allows the users to share storage resources among friends and acquaintances without compromising the security or privacy and enjoying all the benefits that the Cloud storage offers. The system fragments the data and encodes it to securely store it on the unused storage capacity of the data owner's friends' resources. The system thus gives a centralized control to the user over the selection of peers to store the data. Secondly, to retrieve the stored distributed data, the proposed system performs the fusion also from distributed sources. The technique uses several algorithms to ensure the correctness of the query that is used to retrieve and combine the data to improve the information fusion accuracy and efficiency for combining the heterogeneous, distributed and massive data on the Cloud for time critical operations. We demonstrate that the retrieved documents are genuine when the trust scores are also used while retrieving the data sources. The thesis makes several research contributions.
Application of Nomographs for Analysis and Prediction of Receiver Spurious Response EMI (1985)

Abstract : Spurious response EMI for the front end of a superheerodyne receiver follows a simple mathematic formula; however, the application of the formula to predict test frequencies produces more data than can be evaluated. An analysis technique has been developed to graphically depict all receiver spurious responses usig a nomograph and to permit selection of optimum test frequencies. The discussion includes the math model used to simulate a superheterodyne receiver, the implementation of the model in the computer program, the approach to test frequency selection, interpretation of the nomographs, analysis and prediction of receiver spurious response EMI from the nomographs, and application of the nomographs. In addition, figures are provided of sample applications. This EMI analysis and prediction technique greatly improves the Electromagnetic Compatibility (EMC) test engineer's ability to visualize the scope of receiver spurious response EMI testing and optimize test frequency selection. Keywords include: EMI; Receiver spurious response; EMC; and Nomographs.
Analysis of Genetic Variation in 28 Dog Breed Populations With 100 Microsatellite Markers (2003)

Dog breeds were created by man choosing for select phenotypic traits such as size, shape, coat color, conformation, and behavior. Rigorous phenotypic selection likely resulted in a loss of genetic information. The present study extends previous dog population observations by assessing the genotypic variation within and across 28 breeds representing the seven recognized breed groups of the American Kennel Club (AKC). One hundred autosomal microsatellite markers distributed across the canine genome were used to examine variation within breeds. Resulting breed-specific allele frequencies were then used in an attempt to elucidate phylogeny and genetic distances between breeds. While the set of autosomal microsatellites was useful in describing genetic variation within breeds, establishing the genetic relatedness between breeds was less conclusive. A more accurate determination of breed phylogeny will likely require the use of single-nucleotide polymorphisms (SNPs).
<i>Editorials</i>: Parathyroid Hormone Assay Drift: An Unappreciated Problem in Dialysis Patient Management (2005)

The Kidney Disease Outcomes Quality Initiative (K/DOQI) bone metabolism guidelines assume that clinicians use the Nichols intact parathyroid hormone immunoradiometric assay (iPTH IRMA) upon which K/DOQI was based. But for more than a decade, virtually all PTH assay results used for routine end-stage renal disease (ESRD) clinical management have not been generated with this test. Results from the most widely used PTH assays for ESRD patient testing in the United States have varied from 1999 to 2005. The Nichols chemiluminescent Advantage iPTH assay results shifted upwards significantly in 1999 and remained elevated until 2005. From 2003 to 2005, results from the Nichols Advantage Bio-Intact PTH assay shifted upward on average by 29% to 52%. These changes in the most widely used PTH assays have made use of the K/DOQI guidelines with these assays both inappropriate and potentially harmful to patients.
International Knowledge Transfer (2018)

This chapter reviews literature on international knowledge transfer. H. Bresman, J. Birkinshaw and R. Nobel examine the importance of communications and interaction between acquirers and acquiring firms in international knowledge transfer, and they found that face-to-face discussion, as well as frequent visits and regular meetings, facilitate knowledge flows in the post-acquisition period. The chapter reviews the literature on knowledge of the firm, conventional and reverse knowledge transfers. While knowledge sourced from external markets is more open, intra-organisation knowledge is relatively easily understood and assimilated by the receiving units that are foreign subsidiaries, or multinational headquarters in reverse knowledge transfer. The chapter examines the importance of competence-creating subsidiaries. It provides an overview of the importance of absorptive capacity, location choices and language in international knowledge flows. The capacity to absorb the incoming knowledge is treated as an important barrier or facilitator for international transfer within the firm.
Visual Exploration System in an Industrial Context (2016)

This paper describes ExploraTool, a new interactive tool to visually explore data from multiple repositories. The tool has been applied in a real setting to explore computational fluid dynamics (CFD) simulation data and obtain new insights into the space of simulations. The inclusion of free exploration, filtering operations, and chart generation provides a quick method for performance comparisons. The paper proposes an algorithmic means of processing input in the form of tabular data sets, generating a plausible hierarchical structure over metadata categories, which is used to initialize the visualization together with interactions' methods to explore, select, and compare sets of simulation data. This paper also reports on the evaluation study performed involving 24 engineers over two distinct locations from a large automotive manufacturer to evaluate the usability and the overall user satisfaction with the tool. Participants rated the tool as intuitive, useful, and effective.
Phenotype and Outcome in Hereditary Tubulointerstitial Nephritis Secondary to UMOD Mutations (2011)

Hyperuricemia disproportionate to renal function represents the hallmark of renal disease caused by UMOD mutation. Renal survival is highly variable in patients with UMOD mutation. Our data also add novel insights into the interpretation of uricemia and UAEF in patients with chronic kidney diseases.
Studies of DNA dumbbells. IV. Preparation and melting of a DNA dumbbell with the 16 base‐pair sequence <sup>5′</sup>G‐T‐A‐T‐C‐C‐C‐T‐C‐T‐G‐G‐A‐T‐A‐C<sup>3′</sup> linked on the ends by dodecyl chains (1993)

The preparation and melting of a 16 base-pair duplex DNA linked on both ends by C12H24 (dodecyl) chains is described. Absorbance vs temperature curves (optical melting curves) were measured for the dodecyl-linked molecule and the same duplex molecule linked on the ends instead by T4 loops. Optical melting curves of both molecules were measured in 25, 55, and 85 mM Na+ and revealed, regardless of [Na+], the duplex linked by dodecyl loops is more stable by at least 6 degrees C than the same duplex linked by T4 loops. Experimental curves in each salt environment were analyzed in terms of the two-state and multistate theoretical models. In the two-state, or van't Hoff analysis, the melting transition is assumed to occur in an all-or-none manner. Thus, the only possible states accessible to the molecule throughout the melting transition are the completely intact duplex and the completely melted duplex or minicircle. In the multistate analysis no assumptions regarding the melting transition are required and the statistical occurrence of every possible partially melted state of the duplex is explicitly considered. Results of the analysis revealed the melting transitions of both the dodecyl-linked molecule and the dumbbell with T4 end loops are essentially two state in 25 and 55 mM Na+. In contrast, significant deviations from two-state behavior were observed in 85 mM Na+. From our previously published melting data of DNA dumbbells with Tn end loops where n = 2, 3, 4, 6, 8, 10, 14 [T. M. Paner, M. Amaratunga, and A. S. Benight, (1992) Biopolymers, Vol. 32, pp. 881-892] and the dumbbell with T4 end loops of this study, a plot of d(Tm)/d ln [Na+] was constructed. Extrapolation of this data to n = 1 intersects with the value of d (Tm)/d ln [Na+] obtained for the alkyl-linked dumbbell, suggesting the salt-dependent stability of the alkyl-linked molecule behaves as though the duplex of this molecule were linked by end loops comprised of a single T residue.
Orientation-dependent and sequence-specific expansions of CTG/CAG trinucleotide repeats in <i>Saccharomyces cerevisiae</i> (1998)

A quantitative and selective genetic assay was developed to monitor expansions of trinucleotide repeats (TNRs) in yeast. A promoter containing 25 repeats allows expression of a URA3 reporter gene and yields sensitivity to the drug 5-fluoroorotic acid. Expansion of the TNR to 30 or more repeats turns off URA3 and provides drug resistance. When integrated at either of two chromosomal loci, expansion rates were 1 x 10(-5) to 4 x 10(-5) per generation if CTG repeats were replicated on the lagging daughter strand. PCR analysis indicated that 5-28 additional repeats were present in 95% of the expanded alleles. No significant changes in CTG expansion rates occurred in strains deficient in the mismatch repair gene MSH2 or the recombination gene RAD52. The frequent nature of CTG expansions suggests that the threshold number for this repeat is below 25 in this system. In contrast, expansions of the complementary repeat CAG occurred at 500- to 1,000-fold lower rates, similar to a randomized (C,A,G) control sequence. When the reporter plasmid was inverted within the chromosome, switching the leading and lagging strands of replication, frequent expansions were observed only when CTG repeats resided on the lagging daughter strand. Among the rare CAG expansions, the largest gain in tract size was 38 repeats. The control repeats CTA and TAG showed no detectable rate of expansions. The orientation-dependence and sequence-specificity data support the model that expansions of CTG and CAG tracts result from aberrant DNA replication via hairpin-containing Okazaki fragments.
Distribution and Tissue Expression of Semenogelin I and II in Man as Demonstrated by <i>In Situ</i> Hybridization and Immunocytochemistry (1996)

Semenogelin I and II (Sgl, Sgll) are two separate gene products of chromosome 20 with extensive (80%) identity in primary structure. They are mainly responsible for immediate gel formation of freshly ejaculated semen. Degradation of Sgl and Sgll is due to the proteolytic action of prostate-specific antigen (PSA); it results within 5-15 minutes in liquefaction of semen and release of progressively motile spermatozoa. By means of cDNA cloning and Northern blots, Sgl and Sgll transcripts have previously been shown to be abundant in human seminal vesicles, but Sgll alone is suggested to be expressed at low levels in the epididymis. To characterize the expression and tissue distribution of Sgl and Sgll in greater detail, we produced monoclonal immunoglobulin Gs (lgGs for immunocytochemistry (lCC) and specific [35S]-, digoxigenin-, or alkaline phosphatase-labeled 30-mer antisense probes to Sgl and Sgll for in situ hybridization (lSH). Immunocytochemical staining for both Sgl and Sgll, and lSH detection of both Sgl and Sgll transcripts, were demonstrated in the cytoplasm of seminal vesicle epithelium. lSH showed Sgll alone to be expressed in the epithelium of the epididymal cauda. Neither lCC nor lSH yielded any evidence of Sgl or Sgll expression in caput or corpus epithelium or in any stromal cells of the epididymis. Consistent with our previous findings using polyclonal lgG, monoclonal anti-Sgll Sgll lgGs identified epitopes on the posterior head, midpiece, and tail of ejaculated spermatozoa. Spermatozoa in the epididymal cauda were also immunoreactive, but those in the caput or corpus region of the epididymis as well as those in the testis were negative. As shown by lCC, neither Sgl nor Sgll were expressed in the testis, the prostate, the female genital tract, or other normal human tissue specimens. Although the significance of Sg attachment to epididymal and ejaculated spermatozoa remains to be established, monoclonal anti-Sg lgG might prove useful in establishing the origin of seminal vesicle tissue components in prostate core biopsies or other biopsy specimens.
Agar Aerogel Containing Small-Sized Zeolitic Imidazolate Framework Loaded Carbon Nitride: A Solar-Triggered Regenerable Decontaminant for Convenient and Enhanced Water Purification (2017)

Although ZIF-based adsorbents are promising for environmental remediation, their performance is limited by their large crystal size, intrinsic fragility, and poor processability and reusability. To this end, in this work, highly dispersed and small sized (14.95 nm) metal–organic frameworks (MOFs), via the restriction of overgrowth and agglomeration on carbon nitride (C3N4) nanosheets, are integrated into agar aerogel, forming a flexible and efficient aerogel absorbent with photocatalytic activity. This separation-free hybrid aerogel mantaining the crystal structure of zeolitic imidazolate framework (ZIF-8) with smaller size exhibits a 1.44 times greater adsorption capacity for dye than that of pristine bulk ZIF-8. Most importantly, the introduction of C3N4 nanosheets not only regulates the growth of ZIF-8 crystals but also enables the hybdrid aerogel with stable reusability throughout five consecutive adsorption–degradation cycles, obtained via solar irradiation. This ecofriendly, regeneration technology provides a convenient and sustainable approach to reduce the cost and eliminate the use of hazardous substances for environmental remediation. Dramatically, for practical use under sunlight, attributed to the photocatalysis effect of the uniquely designed adsorbent, the active adsorption sites of the aerogel are continuously provided, resulting in enhanced dye removal ability. Therefore, this work establishes an innovative, low-cost, convenient, solar-triggered, sustainable solution for the management of water contamination by a MOF-based aerogel decontaminant.
Risk factors and outcomes of carbapenem‐resistant K lebsiella pneumoniae infections in liver transplant recipients (2015)

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection is increasing in incidence and is associated with increased mortality in liver transplantation (LT) recipients. We performed a retrospective cohort study of all patients transplanted between January 2010 and January 2013 to identify the incidence and risk factors for post-LT CRKP infection and evaluate the impact of this infection on outcomes in a CRKP-endemic area. We studied 304 recipients, of whom 20 (6.6%) developed CRKP and 36 (11.8%) carbapenem-susceptible Klebsiella pneumoniae (CSKP) infections in the year following LT. Among the 20 recipients with post-LT CRKP infection, 8 (40%) were infected in ≥ 2 sites; 13 (65%) had surgical site-intra-abdominal infections; 12 (60%) had pneumonia; and 3 (15%) had a urinary tract infection. There were 6 patients with a CRKP infection before LT, 5 of whom developed a CRKP infection after LT. Significant risk factors for post-LT CRKP infection in multivariate analysis included laboratory Model for End-Stage Liver Disease at LT (odds ratio [OR], 1.07; P = 0.001), hepatocellular carcinoma (OR, 3.19; P = 0.02), Roux-en-Y biliary choledochojejunostomy (OR, 3.15; P = 0.04), and bile leak (OR, 5.89; P = 0.001). One-year estimated patient survival was 55% (95% confidence interval, 31%-73%), 72% (55%-84%), and 93% (89%-96%), for patients with CRKP, CSKP, and no Klebsiella pneumoniae infection, respectively. In multivariate analysis, CRKP (hazard ratio [HR], 6.92; P < 0.001) and CSKP infections (CSKP, HR, 3.84; P < 0.001), as well as bile leak (HR, 2.10; P = 0.03) were the strongest predictors of post-LT mortality. In an endemic area, post-LT CRKP infection is common, occurring in 6.6% of recipients, and is strongly associated with post-LT mortality. Improved strategies for screening and prevention of CRKP infection are urgently needed.
Estimation of Maneuvering Aircraft States and Time-Varying Wind with Turbulence (2012)

Abstract This paper presents an application of the Square Root-Unscented Kalman Filter (SR-UKF) to the estimation of aircraft system states and to the estimation of the total wind vector made up of a time-varying prevailing wind plus turbulence. The estimates are computed using conventional auto-pilot sensors with exponentially correlated measurement errors. The objective of this work is to investigate the convergence limitations of the estimates considering the covariance and correlation time constants of the measurement error models as well as the level of intensity of the turbulence.
Integrated lossless 1 to 4 optical splitter / combiner operating at 1.55 µm (1992)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. A. O. Davies, P. S. Mudhar, M. A. Fisher, D. A. H. Mace, and M. J. Adams, "Integrated lossless 1 to 4 optical splitter / combiner operating at 1.55 µm," in Optical Amplifiers and Their Applications, Vol. 17 of 1992 OSA Technical Digest Series (Optica Publishing Group, 1992), paper PD10. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Rhodium-catalysed [2 + 2 + 2]-cycloadditions of acetylenes (1988)

Wilkinson's catalyst [(PPh3)3RhCl](0.5–2 mol%) catalyses the chemospecific [2 + 2 + 2]-cycloaddition of hepta-1,6-diynes with monoynes to give polysubstituted benzene derivatives in moderate to good yield. The reaction is favoured by polar solvents such as ethanol and occurs at 0–78 °C. Several examples of intramolecular [2 + 2 + 2]-cycloadditions of triynes are described and a mechanism that accounts for the chemospecificity and observed variations in rates of reaction is discussed.
Direct catalytic sulfonation of methane with SO2 to methanesulfonic acid (MSA) in the presence of molecular O2 (2003)

Methane is transformed selectively to methanesulfonic acid at low temperature by liquid-phase sulfonation of methane with SO2 and O2 in the presence of Pd- and Cu-salts as the catalysts.
WASTEWATER MICROBIOLOGY (1976)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
Multiple Optical Carrier Generation from a Supercontinuum Source (2002)

The article reviews the generation of multiple optical carriers from a supercontinuum multicarrier source (SC-MCS). Advantages of SC-MCS include fixed channel spacing with microwave-oscillator (Hz) accuracy and the capability to generate a stream of more than 100 channels. In the future, SC-MCS will play a key role in applications such as WDM systems and optical frequency standards.
Photovoltaic hot spot analysis for cells with various reverse-bias characteristics through electrical and thermal simulation (2013)

Hot spots result from localized heating in a string of photovoltaic (PV) cells due to mismatch that is often caused by partial shading or uneven degradation. Over time, this localized heating can result in permanent damage and degrade string performance. Bypass diodes are commonly employed in PV panels to mitigate this problem, but it does not eradicate the problem-hot spots can still form. This study investigates how the reverse-biased I-V characteristics and number of cells in series affect the potential for hot spotting. Using an electrical and thermal model in Matlab Simulink and Simscape, three distinct PV cells are modeled and simulated in various string lengths. Simulation results confirm that shorter strings reduce hot spot risk, but none of the cell types were immune to hot spotting, particularly in bypass. Bypassing even a short string can lead to hot spots and the temperature rise worsens as string length increases.